Install log for 'AlphaSimR'

* installing *source* package ‘AlphaSimR’ ...
** package ‘AlphaSimR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c MME.cpp -o MME.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c algorithm.cpp -o algorithm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c alphaSuite.cpp -o alphaSuite.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c altAddTraitAD.cpp -o altAddTraitAD.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c calcGenParam.cpp -o calcGenParam.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c datastructures.cpp -o datastructures.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c getGeno.cpp -o getGeno.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c getGv.cpp -o getGv.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c getHybridGv.cpp -o getHybridGv.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c ibd.cpp -o ibd.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c meiosis.cpp -o meiosis.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c misc.cpp -o misc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c optimize.cpp -o optimize.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c packHaplo.cpp -o packHaplo.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/BH/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fPIC  -falign-functions=64 -Wall -g -O2   -c simulator.cpp -o simulator.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o AlphaSimR.so MME.o RcppExports.o algorithm.o alphaSuite.o altAddTraitAD.o calcGenParam.o datastructures.o getGeno.o getGv.o getHybridGv.o ibd.o meiosis.o misc.o optimize.o packHaplo.o simulator.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/AlphaSimR.Rcheck/00LOCK-AlphaSimR/00new/AlphaSimR/libs
** generating debug symbols (dSYM)
** 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
** 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 (AlphaSimR)