##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rsamtools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c PileupBuffer.cpp -o PileupBuffer.o
In file included from PileupBuffer.cpp:1:
./PileupBuffer.h:56:16: warning: private field 'schema' is not used [-Wunused-private-field]
    const SEXP schema, pileupParams, seqnamesLevels;
               ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c PosCacheColl.cpp -o PosCacheColl.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ResultManager.cpp -o ResultManager.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c as_bam.c -o as_bam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam.c -o bam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_data.c -o bam_data.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from bam_mate_iter.cpp:2:
In file included from ./BamRangeIterator.h:7:
./BamIterator.h:87:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
        bam_seek(bfile, 0, 0);
        ^~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include/bam.h:57:32: note: expanded from macro 'bam_seek'
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                               ^~~~~~~~~ ~~~~~~~~~~~~
In file included from bam_mate_iter.cpp:2:
./BamRangeIterator.h:138:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
        bam_seek(bfile, pos, SEEK_SET);
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include/bam.h:57:32: note: expanded from macro 'bam_seek'
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                               ^~~~~~~~~ ~~~~~~~~~~~~
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_sort.c -o bam_sort.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bambuffer.c -o bambuffer.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bamfile.c -o bamfile.o
bamfile.c:168:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
            bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
            ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bcffile.c -o bcffile.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c encode.c -o encode.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fafile.c -o fafile.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c idxstats.c -o idxstats.o
idxstats.c:20:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
    bam_seek(fp, 0, 0);
    ^~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include/bam.h:57:32: note: expanded from macro 'bam_seek'
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                               ^~~~~~~~~ ~~~~~~~~~~~~
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c io_sam.c -o io_sam.o
io_sam.c:304:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
    bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include/bam.h:57:32: note: expanded from macro 'bam_seek'
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                               ^~~~~~~~~ ~~~~~~~~~~~~
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pileup.cpp -o pileup.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pileupbam.c -o pileupbam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam.c -o sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_opts.c -o sam_opts.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_utils.c -o sam_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c samtools_patch.c -o samtools_patch.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c scan_bam_data.c -o scan_bam_data.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -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/4.0/Resources/library/Rhtslib/include/htslib/bgzf.h:243:38: 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/4.0/Resources/library/Rhtslib/include/htslib/hts_defs.h:65:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c tagfilter.c -o tagfilter.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utilities.c -o utilities.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c zip_compression.c -o zip_compression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.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/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/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)