* installing *source* package ‘pcadapt’ ... ** package ‘pcadapt’ 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../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/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../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c af.cpp -o af.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bed-acc-xptr.cpp -o bed-acc-xptr.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bed2matrix.cpp -o bed2matrix.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clumping.cpp -o clumping.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c linear-regression.cpp -o linear-regression.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nb-na.cpp -o nb-na.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedUtils.cpp -o pedUtils.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c prodMat.cpp -o prodMat.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcfUtils.cpp -o vcfUtils.o clang++ -arch arm64 -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-arm64/Rlib/4.3/mmapcharr/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/rmio/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c writebed.cpp -o writebed.o clang++ -arch arm64 -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/arm64/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 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/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/4.3/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)