* installing *source* package ‘pcadapt’ ...
** package ‘pcadapt’ 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../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/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../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c af.cpp -o af.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bed-acc-xptr.cpp -o bed-acc-xptr.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bed2matrix.cpp -o bed2matrix.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clumping.cpp -o clumping.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c linear-regression.cpp -o linear-regression.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nb-na.cpp -o nb-na.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedUtils.cpp -o pedUtils.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c prodMat.cpp -o prodMat.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c total-var.cpp -o total-var.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcfUtils.cpp -o vcfUtils.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c writebed.cpp -o writebed.o
vcfUtils.cpp:84:7: warning: variable 'na_tot' set but not used [-Wunused-but-set-variable]
int na_tot = 0;
^
1 warning generated.
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 pcadapt.so RcppExports.o af.o bed-acc-xptr.o bed2matrix.o clumping.o linear-regression.o nb-na.o pedUtils.o prodMat.o total-var.o vcfUtils.o writebed.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/pcadapt.Rcheck/00LOCK-pcadapt/00new/pcadapt/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 (pcadapt)