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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rbowtie
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Rbowtie’ ...
** using staged installation
** libs
** arch - 
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wall -g -O2   -Wall -g -O2  \""  -Wall -g -O2   -Wall -g -O2    \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
		 -isystem ./SeqAn-1.1 -I third_party \
		-o bowtie-build-s ebwt_build.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
		-L/usr/local/lib  -lz -lpthread 
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wall -g -O2   -Wall -g -O2  \""  -Wall -g -O2   -Wall -g -O2   \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
		 -isystem ./SeqAn-1.1 -I third_party \
		-o bowtie-align-s ebwt_search.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
		-L/usr/local/lib  -lz -lpthread 
In file included from ebwt_search.cpp:29:
./range_cache.h:338:11: warning: private field 'sanity_' is not used [-Wunused-private-field]
        bool     sanity_;  /// do consistency checks?
                 ^
In file included from ebwt_search.cpp:31:
./aligner_0mm.h:118:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
./aligner_0mm.h:348:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
3 warnings generated.
In file included from pat.cpp:9:
./pat.h:743:7: warning: private field 'solexa64_' is not used [-Wunused-private-field]
        bool solexa64_;
             ^
./pat.h:744:7: warning: private field 'phred64_' is not used [-Wunused-private-field]
        bool phred64_;
             ^
./pat.h:745:7: warning: private field 'intQuals_' is not used [-Wunused-private-field]
        bool intQuals_;
             ^
3 warnings generated.
In file included from sam.cpp:13:
./sam.h:119:7: warning: private field 'offBase_' is not used [-Wunused-private-field]
        int  offBase_;        /// Add this to reference offsets before outputting.
             ^
1 warning generated.
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
	make -f Makefile; \
	echo "MAKE of SpliceMap DONE"	
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
runSpliceMap_QuasR.cpp:108:31: warning: unused variable 'chr_file_list_it' [-Wunused-variable]
            vector<string>::iterator chr_file_list_it = chr_file_list.begin();
                                     ^
1 warning generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie)