############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL srnadiff ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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/4.4-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/4.4-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)