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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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

Package 1841/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.22.1  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: RELEASE_3_21
git_last_commit: f06e38b
git_last_commit_date: 2025-04-17 00:30:43 -0400 (Thu, 17 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD BIN results for Rsubread on merida1

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: 2.22.1
Command: rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_2.22.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsubread.buildbin-libdir
StartedAt: 2025-10-14 14:38:20 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 14:40:05 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 105.1 seconds
RetCode: 0
Status:   OK  
PackageFile: Rsubread_2.22.1.tgz
PackageFileSize: 13.21 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_2.22.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsubread.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsubread.buildbin-libdir Rsubread_2.22.1.tar.gz'
>>>>>>> 

* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.22.1’
** 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.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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c cell-counts.c -o cell-counts.o
cell-counts.c:4635:11: 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:4660:11: 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:4734:11: 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:4781:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                size_t frret = fread(&binlen, 1, 4, notmapped_fp);
                       ^
cell-counts.c:4573:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
        srInt_64 removed_umis = 0;
                 ^
5 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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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: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:5700:13: warning: unused variable 'ky_i2' [-Wunused-variable]
        int ky_i1, ky_i2;
                   ^
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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 2.22.1\""  -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 /Users/biocbuild/bbs-3.21-bioc/meat/Rsubread.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so
>>>>>>> 

>>>>>>> Paths before fix:
Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so:
	Rsubread.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"

>>>>>>> Paths after fix:
Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so:
	Rsubread.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)