##############################################################################
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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_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rsubread.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.18.0’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is 36.8Mb
  sub-directories of 1Mb or more:
    annot  30.9Mb
    libs    1.0Mb
    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      94.548 164.764 386.369
propmapped 94.463 164.506 392.005
sublong    29.700   5.222  51.174
buildindex 13.244   2.950  25.089
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rsubread.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c R_wrapper.c -o R_wrapper.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c RsimReads.c -o RsimReads.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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]
        unsigned long long int OVERLAPPED_BASES=0;
                               ^
SNPCalling.c:264:25: warning: variable 'OVER_MISMA_BASES' set but not used [-Wunused-but-set-variable]
        unsigned long long int OVER_MISMA_BASES=0;
                               ^
SNPCalling.c:265:25: warning: variable 'ALL_BASES' set but not used [-Wunused-but-set-variable]
        unsigned long long int ALL_BASES=0;
                               ^
SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
                int window_no = 0;
                    ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c aligner.c -o aligner.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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]
  int line_num = 0;
      ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c cell-counts.c -o cell-counts.o
cell-counts.c:4634:11: 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:4659:11: 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:4733:11: 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:4780:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                size_t frret = fread(&binlen, 1, 4, notmapped_fp);
                       ^
cell-counts.c:4572:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
        srInt_64 removed_umis = 0;
                 ^
5 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-bigtable.c -o core-bigtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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]
        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]
                        int all_reads = 0;
                            ^
core-indel.c:4060:11: warning: variable 'all_indels_in_window' set but not used [-Wunused-but-set-variable]
                                                int all_indels_in_window = 0;
                                                    ^
core-indel.c:3695:6: warning: variable 'global_read_no' set but not used [-Wunused-but-set-variable]
        int global_read_no = 0;
            ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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:4154:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
        int no_sup_juncs = 0;
            ^
core-junction.c:4155:6: warning: variable 'all_juncs' set but not used [-Wunused-but-set-variable]
        int all_juncs = 0;
            ^
core-junction.c:4286:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
        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]
                        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;
                                                                       ^
7 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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]
                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]
        unsigned int linear_cursor = linear;
                     ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detection-calls.c -o detection-calls.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detectionCall.c -o detectionCall.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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]
        int binnum = 0;
            ^
detectionCallAnnotation.c:184:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
        int linenum;
            ^
detectionCallAnnotation.c:274:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
        int linenum;
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align.c -o exon-align.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fullscan.c -o fullscan.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fusion-align.c -o fusion-align.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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]
        int dynamic_delta = 0;
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gene-value-index.c -o gene-value-index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c hashtable.c -o hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c index-builder.c -o index-builder.o
index-builder.c:149:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
                int skips=0, all_skips = 0;
                             ^
index-builder.c:529:10: warning: variable 'read_len' set but not used [-Wunused-but-set-variable]
                int i, read_len = 0;
                       ^
index-builder.c:531:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
                int skips=0, all_skips = 0;
                             ^
index-builder.c:476:23: warning: variable 'read_no' set but not used [-Wunused-but-set-variable]
        unsigned int offset, read_no;
                             ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c input-files.c -o input-files.o
input-files.c:2668:11: warning: variable 'all_orphants' set but not used [-Wunused-but-set-variable]
        srInt_64 all_orphants = 0;
                 ^
input-files.c:2792:6: warning: variable 'current_blocks' set but not used [-Wunused-but-set-variable]
        int current_blocks = 0;
            ^
input-files.c:3242:6: warning: unused variable 'seq_len' [-Wunused-variable]
        int seq_len = qual - seq - 1;
            ^
input-files.c:4922:49: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
        int seq_len = 0, name_len = 0, cigar_opts = 0, block_no=0;
                                                       ^
input-files.c:4923:11: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
        srInt_64 reads =0;
                 ^
input-files.c:5262:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
                unsigned int bam_signature;
                             ^
input-files.c:5572:7: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
                int reads = 0;
                    ^
input-files.c:5801:12: warning: variable 'finished_second_reads' set but not used [-Wunused-but-set-variable]
                srInt_64 finished_second_reads = 0;
                         ^
8 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c interval_merge.c -o interval_merge.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c long-hashtable.c -o long-hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c longread-mapping.c -o longread-mapping.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c mergeVCF.c -o mergeVCF.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c processExons.c -o processExons.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c propmapped.c -o propmapped.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c qualityScores.c -o qualityScores.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c read-repair.c -o read-repair.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c readSummary.c -o readSummary.o
readSummary.c:3804:16: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
                                                srInt_64 assignment_target_number = tmp_voter_id;
                                                         ^
readSummary.c:3874:25: warning: unused variable 'sample_i' [-Wunused-variable]
        int xk1, xk2, ret = 0, sample_i;
                               ^
readSummary.c:5635:45: 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;
                                                   ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -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]
        int chromosome_block_no = 0;
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sam2bed.c -o sam2bed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sambam-file.c -o sambam-file.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c seek-zlib.c -o seek-zlib.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sublog.c -o sublog.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.18.0\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c tx-unique.c -o tx-unique.o
clang -arch arm64 -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 sorted-hashtable.o sublog.o tx-unique.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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)