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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL srnadiff
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘srnadiff’ ...
** 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 C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c rcpp_hmm.cpp -o rcpp_hmm.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c rcpp_ir.cpp -o rcpp_ir.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c rcpp_main.cpp -o rcpp_main.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c rcpp_utils.cpp -o rcpp_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c srnadiff_init.c -o srnadiff_init.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o srnadiff.so RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-srnadiff/00new/srnadiff/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
** testing if installed package keeps a record of temporary installation path
* DONE (srnadiff)