* installing *source* package ‘pedmod’ ...
** package ‘pedmod’ 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 Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c C_FORTRAN_interface.c -o C_FORTRAN_interface.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cdfaprx.cpp -o cdfaprx.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find-tilting-param.cpp -o find-tilting-param.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c graph-partitioning.cpp -o graph-partitioning.o
gfortran -arch x86_64 -fPIC -Wall -g -O2 -c mvt.f -o mvt.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c norm-cdf-approx.cpp -o norm-cdf-approx.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree-ll.cpp -o pedigree-ll.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c qnorm.c -o qnorm.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c qtnorm.cpp -o qtnorm.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c r-api.cpp -o r-api.o
In file included from r-api.cpp:3:
./openmp-exception_ptr.h:12:8: warning: private field 'is_set' is not used [-Wunused-private-field]
bool is_set = false;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sobol.cpp -o sobol.o
sobol.cpp:78:12: warning: unused function 'ibits' [-Wunused-function]
inline int ibits
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-cdfaprx.cpp -o test-cdfaprx.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-find-tilting-param.cpp -o test-find-tilting-param.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-pedigree-ll.cpp -o test-pedigree-ll.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-qtnorm.cpp -o test-qtnorm.o
test-qtnorm.cpp:6:13: warning: unused function 'is_minus_inf' [-Wunused-function]
inline bool is_minus_inf(double const x){
^
test-qtnorm.cpp:9:13: warning: unused function 'is_pos_inf' [-Wunused-function]
inline bool is_pos_inf(double const x){
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/testthat/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/psqn/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threat-safe-random.cpp -o threat-safe-random.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o pedmod.so C_FORTRAN_interface.o RcppExports.o cdfaprx.o find-tilting-param.o graph-partitioning.o mvt.o norm-cdf-approx.o pedigree-ll.o qnorm.o qtnorm.o r-api.o sobol.o test-cdfaprx.o test-find-tilting-param.o test-pedigree-ll.o test-qtnorm.o test-runner.o threat-safe-random.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 -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/4.3/pedmod.Rcheck/00LOCK-pedmod/00new/pedmod/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 (pedmod)