##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rbowtie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Rbowtie’ ...
** this is package ‘Rbowtie’ version ‘1.47.0’
** using staged installation
** libs
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2   -g -O2  \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2   -g -O2    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-02-04T15:03:57\"" -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 \
	 -I third_party -I third_party \
	-o bowtie-build-s ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp  bowtie_build_main.cpp \
	-L/usr/local/lib  -lz -lpthread 
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2   -g -O2  \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2   -g -O2   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-02-04T15:04:14\"" -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 \
	 -I third_party -I third_party \
	-o bowtie-align-s ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
	-L/usr/local/lib  -lz -lpthread 
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"	
make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rbowtie/src/SpliceMap'
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rbowtie/src/SpliceMap'
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)