##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NxtIRFcore
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘NxtIRFcore’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c FastaReader.cpp -o FastaReader.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c GZTools.cpp -o GZTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c IRFinder.cpp -o IRFinder.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:247:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
                unsigned int len=0;
                             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include    -DRNXTIRF -fPIC  -falign-functions=64 -Wall -g -O2  -c covTools.cpp -o covTools.o
clang++ -arch arm64 -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/opt/R/arm64/lib -o NxtIRFcore.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o IRFinder.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o covTools.o -DRNXTIRF -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-NxtIRFcore/00new/NxtIRFcore/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
Warning: Package 'NxtIRFcore' is deprecated and will be removed from
  Bioconductor version 3.18
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'NxtIRFcore' is deprecated and will be removed from
  Bioconductor version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (NxtIRFcore)