Multiple platform build/check report for BioC 3.22 - CHECK results for Rsubread on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 lconway

To the developers/maintainers of the Rsubread package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: Rsubread

Version: 2.23.8

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.23.8.tar.gz

StartedAt: 2025-10-23 23:48:49 -0400 (Thu, 23 Oct 2025)

EndedAt: 2025-10-24 00:03:08 -0400 (Fri, 24 Oct 2025)

EllapsedTime: 858.9 seconds

RetCode: 0

Status: OK

CheckDir: Rsubread.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.23.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rsubread.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.23.8’
* 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 ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
  installed size is 36.9Mb
  sub-directories of 1Mb or more:
    annot  30.9Mb
    libs    1.2Mb
    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 code 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* 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      162.422 195.373 366.606
propmapped 161.837 189.387 360.736
sublong     40.815   6.980  48.014
buildindex  15.628   3.673  19.500
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rsubread.Rcheck/00check.log’
for details.

Installation output

Rsubread.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.8’
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMbase-index.c -o LRMbase-index.o
LRMbase-index.c:146:40: warning: variable 'all_mismatched' set but not used [-Wunused-but-set-variable]
        int read_chrsor = 0, all_matched = 0, all_mismatched = 0;
                                              ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMseek-zlib.c -o LRMseek-zlib.o
LRMseek-zlib.c:194:15: warning: variable 'this_chunk_size' set but not used [-Wunused-but-set-variable]
        unsigned int this_chunk_size = 0;
                     ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c R_wrapper.c -o R_wrapper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c RsimReads.c -o RsimReads.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c SNPCalling.c -o SNPCalling.o
SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
                int window_no = 0;
                    ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c aligner.c -o aligner.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c atgcContent.c -o atgcContent.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c cell-counts.c -o cell-counts.o
cell-counts.c:1147:9: warning: unused variable 'params' [-Wunused-variable]
        void * params [5];
               ^
cell-counts.c:1228:16: warning: variable 'new_details' set but not used [-Wunused-but-set-variable]
        chroEvent_t * new_details = NULL;
                      ^
cell-counts.c:1267:21: warning: variable 'last_start' set but not used [-Wunused-but-set-variable]
        int last_end = -1, last_start = -1;
                           ^
cell-counts.c:1483:23: warning: unused variable 'sample_i' [-Wunused-variable]
        int xk1, edge_tab_i, sample_i;
                             ^
cell-counts.c:2605:132: warning: unused variable 'testi' [-Wunused-variable]
        char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi;
                                                                                                                                          ^
cell-counts.c:3167:30: warning: unused variable 'thread_context' [-Wunused-variable]
        cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                                    ^
cell-counts.c:3248:8: warning: unused variable 'cigar_rlen' [-Wunused-variable]
                        int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar);
                            ^
cell-counts.c:3215:22: warning: unused variable 'x_candidate' [-Wunused-variable]
        int x_3end, x_5end, x_candidate;
                            ^
cell-counts.c:3427:7: warning: unused variable 'read_for_testing_len' [-Wunused-variable]
                int read_for_testing_len = edge_region_end - edge_region_start +1;
                    ^
cell-counts.c:3775:6: warning: unused variable 'retlen' [-Wunused-variable]
        int retlen = general_dynamic_align_moves_to_cigar(result_buffer, moved_len, result_cigar);
            ^
cell-counts.c:3890:10: warning: variable 'rgap' set but not used [-Wunused-but-set-variable]
                                        int rgap = -1;
                                            ^
cell-counts.c:3930:9: warning: unused variable 'manegative' [-Wunused-variable]
                                int manegative = votetab -> masks[mai][maj];
                                    ^
cell-counts.c:3943:9: warning: variable 'rgap' set but not used [-Wunused-but-set-variable]
                                int rgap = -1;
                                    ^
cell-counts.c:3955:9: warning: unused variable 'is_update' [-Wunused-variable]
                                int is_update = cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_JUNCTION, machro, mapos, tstpos, 0, 0);//mapos and tstpos are just borrowed variables. 
                                    ^
cell-counts.c:3839:8: warning: variable 'best_misma_no' set but not used [-Wunused-but-set-variable]
                        int best_misma_no = -1;
                            ^
cell-counts.c:3842:8: warning: variable 'best_GTAG_negative' set but not used [-Wunused-but-set-variable]
                        int best_GTAG_negative = -1;
                            ^
cell-counts.c:3810:31: warning: unused variable 'distinct_vote_number_i' [-Wunused-variable]
        int i,j,reverse_text_offset, distinct_vote_number_i;
                                     ^
cell-counts.c:3810:10: warning: unused variable 'reverse_text_offset' [-Wunused-variable]
        int i,j,reverse_text_offset, distinct_vote_number_i;
                ^
cell-counts.c:4053:9: warning: variable 'on_chro_len' set but not used [-Wunused-but-set-variable]
                                int on_chro_len = tmpi +1;
                                    ^
cell-counts.c:4084:24: warning: variable 'x2_not_matter' set but not used [-Wunused-but-set-variable]
                                                int is_the_last, x2_not_matter;
                                                                 ^
cell-counts.c:4118:46: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                        IVT_IntervalTreeNode * myroot = LR_roots[LRi];
                                                                                ^~~~
cell-counts.c:4010:34: warning: unused variable 'x3' [-Wunused-variable]
        int nch, tmpi=0, x1=0, b1off=0, x3;
                                        ^
cell-counts.c:6279:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(&section1_items,1, 8, input_fps[xk1]);
                               ^
cell-counts.c:6304:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
                               ^
cell-counts.c:6378:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(last_rbin_buffer[selected_fp_no]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[selected_fp_no]);
                               ^
cell-counts.c:6425:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                size_t frret = fread(&binlen, 1, 4, notmapped_fp);
                       ^
cell-counts.c:6217:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
        srInt_64 removed_umis = 0;
                 ^
cell-counts.c:6961:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
                int unique_junctions = 0;
                    ^
cell-counts.c:6904:6: warning: unused variable 'infile_i' [-Wunused-variable]
        int infile_i, disk_is_full = 0, sample_i;
            ^
cell-counts.c:6938:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
        char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
                                                                                ^
cell-counts.c:6940:6: warning: unused variable 'ky_i1' [-Wunused-variable]
        int ky_i1, ky_i2;
            ^
cell-counts.c:6940:13: warning: unused variable 'ky_i2' [-Wunused-variable]
        int ky_i1, ky_i2;
                   ^
32 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-bigtable.c -o core-bigtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-indel.c -o core-indel.o
core-indel.c:2592:8: warning: variable 'all_reads' set but not used [-Wunused-but-set-variable]
                        int all_reads = 0;
                            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-junction.c -o core-junction.o
core-junction.c:3166:6: warning: variable 'total_perfect_matched_sections' set but not used [-Wunused-but-set-variable]
        int total_perfect_matched_sections = 0;
            ^
core-junction.c:4764:8: warning: variable 'coverage_len' set but not used [-Wunused-but-set-variable]
                        int coverage_len = max_end - max_start + vote->coverage_end[i][j] - vote->coverage_start[i][j];
                            ^
core-junction.c:5728:13: warning: variable 'small_dist' set but not used [-Wunused-but-set-variable]
                long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
                          ^
core-junction.c:5728:58: warning: variable 'large_dist' set but not used [-Wunused-but-set-variable]
                long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
                                                                       ^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core.c -o core.o
core.c:1373:15: warning: variable 'linear_cursor' set but not used [-Wunused-but-set-variable]
        unsigned int linear_cursor = linear;
                     ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detection-calls.c -o detection-calls.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detectionCall.c -o detectionCall.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align.c -o exon-align.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fullscan.c -o fullscan.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fusion-align.c -o fusion-align.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gene-algorithms.c -o gene-algorithms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gene-value-index.c -o gene-value-index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c hashtable.c -o hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c index-builder.c -o index-builder.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c input-blc.c -o input-blc.o
input-blc.c:580:17: warning: unused variable 'npos' [-Wunused-variable]
                                                long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
                                                          ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c input-files.c -o input-files.o
input-files.c:2670:11: warning: variable 'all_orphants' set but not used [-Wunused-but-set-variable]
        srInt_64 all_orphants = 0;
                 ^
input-files.c:3244:6: warning: unused variable 'seq_len' [-Wunused-variable]
        int seq_len = qual - seq - 1;
            ^
input-files.c:5289:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
                unsigned int bam_signature;
                             ^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c interval_merge.c -o interval_merge.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c long-hashtable.c -o long-hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c longread-mapping.c -o longread-mapping.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c mergeVCF.c -o mergeVCF.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c processExons.c -o processExons.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c propmapped.c -o propmapped.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c qualityScores.c -o qualityScores.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c read-repair.c -o read-repair.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c readSummary.c -o readSummary.o
readSummary.c:3900:16: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
                                                srInt_64 assignment_target_number = tmp_voter_id;
                                                         ^
readSummary.c:3970:25: warning: unused variable 'sample_i' [-Wunused-variable]
        int xk1, xk2, ret = 0, sample_i;
                               ^
readSummary.c:5724:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
                int unique_junctions = 0;
                    ^
readSummary.c:5700:13: warning: unused variable 'ky_i2' [-Wunused-variable]
        int ky_i1, ky_i2;
                   ^
readSummary.c:5698:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
        char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
                                                                                ^
readSummary.c:5700:6: warning: unused variable 'ky_i1' [-Wunused-variable]
        int ky_i1, ky_i2;
            ^
readSummary.c:5971:45: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
        int  isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
                                                   ^
7 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c removeDupReads.c -o removeDupReads.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sam2bed.c -o sam2bed.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sambam-file.c -o sambam-file.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c seek-zlib.c -o seek-zlib.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sublog.c -o sublog.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.8\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c tx-unique.c -o tx-unique.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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

name	user	system	elapsed
align	162.422	195.373	366.606
buildindex	15.628	3.673	19.500
cellCounts	0.000	0.000	0.001
featureCounts	0	0	0
findCommonVariants	0.000	0.000	0.001
getInBuiltAnnotation	0.363	0.025	0.391
promoterRegions	1.804	0.051	1.875
propmapped	161.837	189.387	360.736
qualityScores	0.062	0.007	0.070
simReads	0	0	0
sublong	40.815	6.980	48.014