Install log for 'Eagle'

* installing *source* package ‘Eagle’ ...
** package ‘Eagle’ 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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c CreateASCIInospace.cpp -o CreateASCIInospace.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c CreateASCIInospace_PLINK.cpp -o CreateASCIInospace_PLINK.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c CreateBIN.cpp -o CreateBIN.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c CreateBIN_PLINK.cpp -o CreateBIN_PLINK.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c ReadBlock.cpp -o ReadBlock.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c ReadBlockBin.cpp -o ReadBlockBin.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c ReshapeM_rcpp.cpp -o ReshapeM_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c calculateMMt_rcpp.cpp -o calculateMMt_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c calculate_a_and_vara_batch_rcpp.cpp -o calculate_a_and_vara_batch_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c calculate_a_and_vara_rcpp.cpp -o calculate_a_and_vara_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c calculate_reduced_a_rcpp.cpp -o calculate_reduced_a_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c createM_ASCII_rcpp.cpp -o createM_ASCII_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c createM_BIN_rcpp.cpp -o createM_BIN_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c createMt_ASCII_rcpp.cpp -o createMt_ASCII_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c createMt_BIN_rcpp.cpp -o createMt_BIN_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c create_vcf_BIN_rcpp.cpp -o create_vcf_BIN_rcpp.o
create_vcf_BIN_rcpp.cpp:11:14: warning: unused variable 'bits_in_int' [-Wunused-const-variable]
const size_t bits_in_int = std::numeric_limits<int>::digits;
             ^
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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c extract_geno_Mt_rcpp.cpp -o extract_geno_Mt_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c extract_geno_rcpp.cpp -o extract_geno_rcpp.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c fasttimer.cpp -o fasttimer.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c getNumColumns.cpp -o getNumColumns.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c getNumRows.cpp -o getNumRows.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c getRowColumn.cpp -o getRowColumn.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c removeColumn.cpp -o removeColumn.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/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I/opt/R/arm64/include   -DEIGEN_USE_BLAS  -fPIC  -falign-functions=64 -Wall -g -O2   -c removeRow.cpp -o removeRow.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 Eagle.so CreateASCIInospace.o CreateASCIInospace_PLINK.o CreateBIN.o CreateBIN_PLINK.o RcppExports.o ReadBlock.o ReadBlockBin.o ReshapeM_rcpp.o calculateMMt_rcpp.o calculate_a_and_vara_batch_rcpp.o calculate_a_and_vara_rcpp.o calculate_reduced_a_rcpp.o createM_ASCII_rcpp.o createM_BIN_rcpp.o createMt_ASCII_rcpp.o createMt_BIN_rcpp.o create_vcf_BIN_rcpp.o extract_geno_Mt_rcpp.o extract_geno_rcpp.o fasttimer.o getNumColumns.o getNumRows.o getRowColumn.o removeColumn.o removeRow.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/4.4/Eagle.Rcheck/00LOCK-Eagle/00new/Eagle/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 (Eagle)