Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1770/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 2.16.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Rsamtools
git_branch: RELEASE_3_17
git_last_commit: 3eb6d03
git_last_commit_date: 2023-04-25 09:50:37 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for Rsamtools on kjohnson2


To the developers/maintainers of the Rsamtools package:
- 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: Rsamtools
Version: 2.16.0
Command: rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsamtools_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsamtools.buildbin-libdir
StartedAt: 2023-10-19 16:43:50 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 16:45:36 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 105.8 seconds
RetCode: 0
Status:   OK  
PackageFile: Rsamtools_2.16.0.tgz
PackageFileSize: 3.961 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsamtools_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsamtools.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_2.16.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PileupBuffer.cpp -o PileupBuffer.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PosCacheColl.cpp -o PosCacheColl.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ResultManager.cpp -o ResultManager.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c as_bam.c -o as_bam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_data.c -o bam_data.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_mate_iter.cpp -o bam_mate_iter.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_sort.c -o bam_sort.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bambuffer.c -o bambuffer.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bamfile.c -o bamfile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bcffile.c -o bcffile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bedidx.c -o bedidx.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c encode.c -o encode.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fafile.c -o fafile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c idxstats.c -o idxstats.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c io_sam.c -o io_sam.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pileup.cpp -o pileup.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pileupbam.c -o pileupbam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sam_opts.c -o sam_opts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sam_utils.c -o sam_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c samtools_patch.c -o samtools_patch.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c scan_bam_data.c -o scan_bam_data.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tabixfile.c -o tabixfile.o
tabixfile.c:190:9: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
    if (bgzf_is_bgzf(fn) != 1)
        ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include/htslib/bgzf.h:270:38: note: 'bgzf_is_bgzf' has been explicitly marked deprecated here
    int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
                                     ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c tagfilter.c -o tagfilter.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utilities.c -o utilities.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c zip_compression.c -o zip_compression.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rsamtools.buildbin-libdir/00LOCK-Rsamtools/00new/Rsamtools/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 (Rsamtools)


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

>>>>>>> Paths before fix:
Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so:
	Rsamtools.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so"

>>>>>>> Paths after fix:

Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so:
	Rsamtools.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)