* installing *source* package ‘pagoda2’ ...
** package ‘pagoda2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c binaryExport.cpp -o binaryExport.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c checkfunctions.cpp -o checkfunctions.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c edgeweights.cpp -o edgeweights.o
edgeweights.cpp:123:12: warning: variable 'sum_weight' set but not used [-Wunused-but-set-variable]
double sum_weight = 0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c gradients.cpp -o gradients.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c largeVis.cpp -o largeVis.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c misc2.cpp -o misc2.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c pagoda1_liftover.cpp -o pagoda1_liftover.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I/opt/R/arm64/include -I"./include" -fPIC -falign-functions=64 -Wall -g -O2 -c rank.cpp -o rank.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o pagoda2.so RcppExports.o binaryExport.o checkfunctions.o edgeweights.o gradients.o largeVis.o misc2.o pagoda1_liftover.o rank.o -L. -lpthread -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/pagoda2.Rcheck/00LOCK-pagoda2/00new/pagoda2/libs
** generating debug symbols (dSYM)
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pagoda2)