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This page was generated on 2026-03-21 11:35 -0400 (Sat, 21 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4866
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" 4545
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Package 1862/2368HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.25.2  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2026-03-20 13:40 -0400 (Fri, 20 Mar 2026)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: devel
git_last_commit: a268154
git_last_commit_date: 2026-03-17 19:02:05 -0400 (Tue, 17 Mar 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    ERROR  
See other builds for Rsubread in R Universe.

CHECK results for Rsubread on kjohnson3

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: 2.25.2
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_2.25.2.tar.gz
StartedAt: 2026-03-21 01:02:46 -0400 (Sat, 21 Mar 2026)
EndedAt: 2026-03-21 01:04:31 -0400 (Sat, 21 Mar 2026)
EllapsedTime: 105.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rsubread.Rcheck
Warnings: 4

Command output

##############################################################################
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###
### 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_2.25.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-21 05:02:46 UTC
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.25.2’
* 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:3530:2: warning: "======= THIS IS FOR DEBUGGING CRASH ('__DEBUG_NO_LOOK') =======" [-W#warnings]
  cell-counts.c:5536:4: warning: "=====  DISABLED TABLE_BASED BATCHING !!! =====" [-W#warnings]
  cell-counts.c:5677:171: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
  cell-counts.c:5677:175: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
  cell-counts.c:6513:112: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... INFO
  installed size is 36.8Mb
  sub-directories of 1Mb or more:
    annot  30.9Mb
    libs    1.1Mb
    qualf   3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 ... WARNING
Codoc mismatches from Rd file 'cellCounts.Rd':
cellCounts
  Code: function(index, sample, input.mode = "BCL", cell.barcode =
                 NULL, nsubreads = 15, minVotes = 1, maxMismatches =
                 10, minMappedLength = 1, annot.inbuilt = "mm39",
                 annot.ext = NULL, isGTFAnnotationFile = FALSE,
                 GTF.featureType = "exon", GTF.attrType = "gene_id",
                 useMetaFeatures = TRUE, detectJunctions = FALSE,
                 umi.cutoff = NULL, nthreads = 10, nBestLocations = 1,
                 uniqueMapping = FALSE, reportExcludedBarcodes = FALSE,
                 barcoding.mode = "Chromium", cell.level.junctions =
                 NULL, cell.cluster.map = NULL)
  Docs: function(index, sample, input.mode = "BCL", cell.barcode =
                 NULL, nsubreads = 15, minVotes = 1, maxMismatches =
                 10, minMappedLength = 1, annot.inbuilt = "mm39",
                 annot.ext = NULL, isGTFAnnotationFile = FALSE,
                 GTF.featureType = "exon", GTF.attrType = "gene_id",
                 useMetaFeatures = TRUE, detectJunctions = FALSE,
                 umi.cutoff = NULL, nthreads = 10, nBestLocations = 1,
                 uniqueMapping = FALSE, reportExcludedBarcodes = FALSE)
  Argument names in code not in docs:
    barcoding.mode cell.level.junctions cell.cluster.map

* checking Rd \usage sections ... WARNING
Assignments in \usage in Rd file 'simReads.Rd':
  simplify.transcript.names = FALSE

Bad \usage lines found in Rd file 'simReads.Rd':
  simReads(
      transcript.file,
      expression.levels,
      output.prefix,
      library.size = 1e5,
      read.length = 75,
      truth.in.read.names = FALSE,
      simulate.sequencing.error = TRUE,
      quality.reference = NULL,
      paired.end = FALSE,
      fragment.length.min = 100,
      fragment.length.max = 500,
      fragment.length.mean = 180,
      fragment.length.sd = 40,
      strandSpecific = 0)
  scanFasta(
      transcript.file,
      simplify.transcript.names = FALSE,
      quiet = FALSE)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rsubread/libs/Rsubread.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking 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      21.837  2.601  25.797
propmapped 21.928  2.224  25.326
sublong    12.272  1.947  14.750
buildindex  6.096  1.332   7.868
* 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: 4 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck/00check.log’
for details.

Installation output

Rsubread.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.25.2’
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
HelperFunctions.c:2991:16: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
 2991 |         M[k] = NEG_INF;
      |                ^~~~~~~
HelperFunctions.c:2939:23: note: expanded from macro 'NEG_INF'
 2939 | #define NEG_INF (-1LL << 60)
      |                  ~~~~ ^
HelperFunctions.c:2992:17: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
 2992 |         Ix[k] = NEG_INF;
      |                 ^~~~~~~
HelperFunctions.c:2939:23: note: expanded from macro 'NEG_INF'
 2939 | #define NEG_INF (-1LL << 60)
      |                  ~~~~ ^
HelperFunctions.c:2993:17: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
 2993 |         Iy[k] = NEG_INF;
      |                 ^~~~~~~
HelperFunctions.c:2939:23: note: expanded from macro 'NEG_INF'
 2939 | #define NEG_INF (-1LL << 60)
      |                  ~~~~ ^
3 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -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]
  146 |         int read_chrsor = 0, all_matched = 0, all_mismatched = 0;
      |                                               ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -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]
  194 |         unsigned int this_chunk_size = 0;
      |                      ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c R_wrapper.c -o R_wrapper.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c RsimReads.c -o RsimReads.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c SNPCalling.c -o SNPCalling.o
SNPCalling.c:263:25: warning: variable 'OVERLAPPED_BASES' set but not used [-Wunused-but-set-variable]
  263 |         unsigned long long int OVERLAPPED_BASES=0;
      |                                ^
SNPCalling.c:264:25: warning: variable 'OVER_MISMA_BASES' set but not used [-Wunused-but-set-variable]
  264 |         unsigned long long int OVER_MISMA_BASES=0;
      |                                ^
SNPCalling.c:265:25: warning: variable 'ALL_BASES' set but not used [-Wunused-but-set-variable]
  265 |         unsigned long long int ALL_BASES=0;
      |                                ^
SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
  707 |                 int window_no = 0;
      |                     ^
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c aligner.c -o aligner.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c atgcContent.c -o atgcContent.o
atgcContent.c:72:7: warning: variable 'line_num' set but not used [-Wunused-but-set-variable]
   72 |   int line_num = 0;
      |       ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c cell-counts.c -o cell-counts.o
cell-counts.c:1180:9: warning: unused variable 'params' [-Wunused-variable]
 1180 |         void * params [5];
      |                ^~~~~~
cell-counts.c:1263:16: warning: variable 'new_details' set but not used [-Wunused-but-set-variable]
 1263 |         chroEvent_t * new_details = NULL;
      |                       ^
cell-counts.c:1317:21: warning: variable 'last_start' set but not used [-Wunused-but-set-variable]
 1317 |         int last_end = -1, last_start = -1;
      |                            ^
cell-counts.c:1523:23: warning: unused variable 'sample_i' [-Wunused-variable]
 1523 |         int xk1, edge_tab_i, sample_i;
      |                              ^~~~~~~~
cell-counts.c:2823:132: warning: unused variable 'testi' [-Wunused-variable]
 2823 |         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:3394:30: warning: unused variable 'thread_context' [-Wunused-variable]
 3394 |         cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
      |                                     ^~~~~~~~~~~~~~
cell-counts.c:3530:2: warning: "======= THIS IS FOR DEBUGGING CRASH ('__DEBUG_NO_LOOK') =======" [-W#warnings]
 3530 | #warning "======= THIS IS FOR DEBUGGING CRASH ('__DEBUG_NO_LOOK') ======="
      |  ^
cell-counts.c:3520:8: warning: unused variable 'cigar_rlen' [-Wunused-variable]
 3520 |                         int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar,&sum_ins);
      |                             ^~~~~~~~~~
cell-counts.c:3470:22: warning: unused variable 'x_candidate' [-Wunused-variable]
 3470 |         int x_3end, x_5end, x_candidate;
      |                             ^~~~~~~~~~~
cell-counts.c:3723:7: warning: unused variable 'read_for_testing_len' [-Wunused-variable]
 3723 |                 int read_for_testing_len = edge_region_end - edge_region_start +1;
      |                     ^~~~~~~~~~~~~~~~~~~~
cell-counts.c:3829:132: warning: unused variable 'testi' [-Wunused-variable]
 3829 |         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:4092:6: warning: unused variable 'retlen' [-Wunused-variable]
 4092 |         int retlen = general_dynamic_align_moves_to_cigar(result_buffer, moved_len, result_cigar);
      |             ^~~~~~
cell-counts.c:4205:10: warning: variable 'rgap' set but not used [-Wunused-but-set-variable]
 4205 |                                         int rgap = -1;
      |                                             ^
cell-counts.c:4245:9: warning: unused variable 'manegative' [-Wunused-variable]
 4245 |                                 int manegative = votetab -> masks[mai][maj];
      |                                     ^~~~~~~~~~
cell-counts.c:4157:8: warning: variable 'best_GTAG_negative' set but not used [-Wunused-but-set-variable]
 4157 |                         int best_GTAG_negative = -1;
      |                             ^
cell-counts.c:4127:10: warning: unused variable 'reverse_text_offset' [-Wunused-variable]
 4127 |         int i,j,reverse_text_offset, distinct_vote_number_i;
      |                 ^~~~~~~~~~~~~~~~~~~
cell-counts.c:4127:31: warning: unused variable 'distinct_vote_number_i' [-Wunused-variable]
 4127 |         int i,j,reverse_text_offset, distinct_vote_number_i;
      |                                      ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4373:9: warning: variable 'on_chro_len' set but not used [-Wunused-but-set-variable]
 4373 |                                 int on_chro_len = tmpi +1;
      |                                     ^
cell-counts.c:4404:24: warning: variable 'x2_not_matter' set but not used [-Wunused-but-set-variable]
 4404 |                                                 int is_the_last, x2_not_matter;
      |                                                                  ^
cell-counts.c:4438:46: warning: array subscript is of type 'char' [-Wchar-subscripts]
 4438 |                                         IVT_IntervalTreeNode * myroot = LR_roots[LRi];
      |                                                                                 ^~~~
cell-counts.c:4328:34: warning: unused variable 'x3' [-Wunused-variable]
 4328 |         int nch, tmpi=0, x1=0, b1off=0, x3;
      |                                         ^~
cell-counts.c:5079:6: warning: variable 'preads' set but not used [-Wunused-but-set-variable]
 5079 |         int preads=0;
      |             ^
cell-counts.c:5536:4: warning: "=====  DISABLED TABLE_BASED BATCHING !!! =====" [-W#warnings]
 5536 |                 #warning "=====  DISABLED TABLE_BASED BATCHING !!! ====="
      |                  ^
cell-counts.c:5677:171: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
 5677 | fprintf(stderr,"STEP_%d_FINN_X1: %.10s  gene_no=%016lld  supReads=%d  start=%d,%d  CELL_BC=%d CHANGED=%d\n", is_UMI_step2+1, str1->umi, str1 -> gene_no, str1->supp_reads,x1, sec_start, str1->cellbc, is_umi_changed);
      |                                                                             ~~                                                                                            ^~
      |                                                                             %lld
cell-counts.c:5677:175: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
 5677 | fprintf(stderr,"STEP_%d_FINN_X1: %.10s  gene_no=%016lld  supReads=%d  start=%d,%d  CELL_BC=%d CHANGED=%d\n", is_UMI_step2+1, str1->umi, str1 -> gene_no, str1->supp_reads,x1, sec_start, str1->cellbc, is_umi_changed);
      |                                                                                ~~                                                                                             ^~~~~~~~~
      |                                                                                %lld
cell-counts.c:5676:29: warning: unused variable 'str2' [-Wunused-variable]
 5676 | struct cell_gene_umi_supp * str2 = ArrayListGet(structs, sec_start +1);
      |                             ^~~~
cell-counts.c:6513:112: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
 6513 | fprintf(stderr,"%dth resample: BOOT_30TH: %lld UMI / %lld cells. Top UMIs (original/resampled) %lld  %lld \n", x1, UMIs_30th_div10,  list_cellBCs_sorted_by_UMIs -> numOfElements, ori_umis , top_umis);
      |                 ~~                                                                                             ^~
      |                 %lld
cell-counts.c:6729:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
 6729 |                         size_t frret = fread(&section1_items,1, 8, input_fps[xk1]);
      |                                ^
cell-counts.c:6754:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
 6754 |                         size_t frret = fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
      |                                ^
cell-counts.c:6828:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
 6828 |                         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:6875:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
 6875 |                 size_t frret = fread(&binlen, 1, 4, notmapped_fp);
      |                        ^
cell-counts.c:6667:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
 6667 |         srInt_64 removed_umis = 0;
      |                  ^
cell-counts.c:7411:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
 7411 |                 int unique_junctions = 0;
      |                     ^~~~~~~~~~~~~~~~
cell-counts.c:7354:6: warning: unused variable 'infile_i' [-Wunused-variable]
 7354 |         int infile_i, disk_is_full = 0, sample_i;
      |             ^~~~~~~~
cell-counts.c:7388:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
 7388 |         char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
      |                                                                                 ^~~~~~~~~~~~~~
cell-counts.c:7390:6: warning: unused variable 'ky_i1' [-Wunused-variable]
 7390 |         int ky_i1, ky_i2;
      |             ^~~~~
cell-counts.c:7390:13: warning: unused variable 'ky_i2' [-Wunused-variable]
 7390 |         int ky_i1, ky_i2;
      |                    ^~~~~
37 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-bigtable.c -o core-bigtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-indel.c -o core-indel.o
core-indel.c:455:32: warning: variable 'all_junctions' set but not used [-Wunused-but-set-variable]
  455 |         int to_be_removed_number = 0, all_junctions = 0;
      |                                       ^
core-indel.c:2592:8: warning: variable 'all_reads' set but not used [-Wunused-but-set-variable]
 2592 |                         int all_reads = 0;
      |                             ^
core-indel.c:4060:11: warning: variable 'all_indels_in_window' set but not used [-Wunused-but-set-variable]
 4060 |                                                 int all_indels_in_window = 0;
      |                                                     ^
core-indel.c:3695:6: warning: variable 'global_read_no' set but not used [-Wunused-but-set-variable]
 3695 |         int global_read_no = 0;
      |             ^
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -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]
 3166 |         int total_perfect_matched_sections = 0;
      |             ^
core-junction.c:4154:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
 4154 |         int no_sup_juncs = 0;
      |             ^
core-junction.c:4155:6: warning: variable 'all_juncs' set but not used [-Wunused-but-set-variable]
 4155 |         int all_juncs = 0;
      |             ^
core-junction.c:4286:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
 4286 |         int no_sup_juncs = 0, disk_is_full = 0;
      |             ^
core-junction.c:4764:8: warning: variable 'coverage_len' set but not used [-Wunused-but-set-variable]
 4764 |                         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]
 5728 |                 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]
 5728 |                 long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
      |                                                                        ^
7 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core.c -o core.o
core.c:184:79: warning: variable 'real_lenwidth' set but not used [-Wunused-but-set-variable]
  184 |                 int is_R_code,x1,content_len = strlen(content), state, txt_len, is_cut = 0, real_lenwidth;
      |                                                                                             ^
core.c:1373:15: warning: variable 'linear_cursor' set but not used [-Wunused-but-set-variable]
 1373 |         unsigned int linear_cursor = linear;
      |                      ^
2 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detection-calls.c -o detection-calls.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detectionCall.c -o detectionCall.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c:154:6: warning: variable 'binnum' set but not used [-Wunused-but-set-variable]
  154 |         int binnum = 0;
      |             ^
detectionCallAnnotation.c:184:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
  184 |         int linenum;
      |             ^
detectionCallAnnotation.c:274:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
  274 |         int linenum;
      |             ^
3 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align.c -o exon-align.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fullscan.c -o fullscan.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fusion-align.c -o fusion-align.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c:795:6: warning: variable 'dynamic_delta' set but not used [-Wunused-but-set-variable]
  795 |         int dynamic_delta = 0;
      |             ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gene-value-index.c -o gene-value-index.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c hashtable.c -o hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c index-builder.c -o index-builder.o
index-builder.c:157:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
  157 |                 int skips=0, all_skips = 0;
      |                              ^
index-builder.c:543:10: warning: variable 'read_len' set but not used [-Wunused-but-set-variable]
  543 |                 int i, read_len = 0;
      |                        ^
index-builder.c:545:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
  545 |                 int skips=0, all_skips = 0;
      |                              ^
index-builder.c:490:23: warning: variable 'read_no' set but not used [-Wunused-but-set-variable]
  490 |         unsigned int offset, read_no;
      |                              ^
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c input-blc.c -o input-blc.o
input-blc.c:585:17: warning: unused variable 'npos' [-Wunused-variable]
  585 |                                                 long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
      |                                                           ^~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -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]
 2670 |         srInt_64 all_orphants = 0;
      |                  ^
input-files.c:2794:6: warning: variable 'current_blocks' set but not used [-Wunused-but-set-variable]
 2794 |         int current_blocks = 0;
      |             ^
input-files.c:3244:6: warning: unused variable 'seq_len' [-Wunused-variable]
 3244 |         int seq_len = qual - seq - 1;
      |             ^~~~~~~
input-files.c:4953:49: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
 4953 |         int seq_len = 0, name_len = 0, cigar_opts = 0, block_no=0;
      |                                                        ^
input-files.c:4954:11: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
 4954 |         srInt_64 reads =0;
      |                  ^
input-files.c:5289:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
 5289 |                 unsigned int bam_signature;
      |                              ^
input-files.c:5599:7: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
 5599 |                 int reads = 0;
      |                     ^
input-files.c:5828:12: warning: variable 'finished_second_reads' set but not used [-Wunused-but-set-variable]
 5828 |                 srInt_64 finished_second_reads = 0;
      |                          ^
8 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c interval_merge.c -o interval_merge.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c long-hashtable.c -o long-hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c longread-mapping.c -o longread-mapping.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c mergeVCF.c -o mergeVCF.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c processExons.c -o processExons.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c propmapped.c -o propmapped.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c qualityScores.c -o qualityScores.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c read-repair.c -o read-repair.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -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]
 3900 |                                                 srInt_64 assignment_target_number = tmp_voter_id;
      |                                                          ^
readSummary.c:3970:25: warning: unused variable 'sample_i' [-Wunused-variable]
 3970 |         int xk1, xk2, ret = 0, sample_i;
      |                                ^~~~~~~~
readSummary.c:5724:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
 5724 |                 int unique_junctions = 0;
      |                     ^~~~~~~~~~~~~~~~
readSummary.c:5698:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
 5698 |         char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
      |                                                                                 ^~~~~~~~~~~~~~
readSummary.c:5700:6: warning: unused variable 'ky_i1' [-Wunused-variable]
 5700 |         int ky_i1, ky_i2;
      |             ^~~~~
readSummary.c:5700:13: warning: unused variable 'ky_i2' [-Wunused-variable]
 5700 |         int ky_i1, ky_i2;
      |                    ^~~~~
readSummary.c:5971:45: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
 5971 |         int  isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
      |                                                    ^
7 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c removeDupReads.c -o removeDupReads.o
removeDupReads.c:71:6: warning: variable 'chromosome_block_no' set but not used [-Wunused-but-set-variable]
   71 |         int chromosome_block_no = 0;
      |             ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sam2bed.c -o sam2bed.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sambam-file.c -o sambam-file.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c seek-zlib.c -o seek-zlib.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c softclip-test.c -o softclip-test.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sublog.c -o sublog.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.25.2\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c tx-unique.c -o tx-unique.o
clang -arch arm64 -std=gnu23 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 softclip-test.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/4.6/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

nameusersystemelapsed
align21.837 2.60125.797
buildindex6.0961.3327.868
cellCounts000
featureCounts000
findCommonVariants0.0000.0000.001
getInBuiltAnnotation0.1550.0080.169
promoterRegions0.8130.0140.859
propmapped21.928 2.22425.326
qualityScores0.0200.0020.023
simReads000
sublong12.272 1.94714.750