* installing *source* package ‘bigsnpr’ ...
** package ‘bigsnpr’ 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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -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'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c bed-fun.cpp -o bed-fun.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c bed-mat-acc.cpp -o bed-mat-acc.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c bed-prod-vec.cpp -o bed-prod-vec.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c clumping-bed.cpp -o clumping-bed.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c clumping-cached.cpp -o clumping-cached.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -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'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c colstats.cpp -o colstats.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c copy-subset.cpp -o copy-subset.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c corr.cpp -o corr.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c corr_with_cov.cpp -o corr_with_cov.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c impute-simple.cpp -o impute-simple.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c lassosum2.cpp -o lassosum2.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c ld-scores-sfbm.cpp -o ld-scores-sfbm.o
corr.cpp:24:7: warning: unused variable 'chunk_size' [-Wunused-variable]
int chunk_size = ceil(m / (10.0 * ncores));
^
ld-scores-sfbm.cpp:25:7: warning: unused variable 'chunk_size' [-Wunused-variable]
int chunk_size = ceil(m / (10.0 * ncores));
^
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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c ld-scores.cpp -o ld-scores.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c ldpred2-auto.cpp -o ldpred2-auto.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c ldpred2-sampling.cpp -o ldpred2-sampling.o
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/4.4/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c ldpred2.cpp -o ldpred2.o
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/4.4/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c multLinReg.cpp -o multLinReg.o
ld-scores.cpp:22:7: warning: unused variable 'chunk_size' [-Wunused-variable]
int chunk_size = ceil(m / (10.0 * ncores));
^
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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c prod-bgen.cpp -o prod-bgen.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c project-utils.cpp -o project-utils.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c read-bgen.cpp -o read-bgen.o
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/4.4/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c read-plink.cpp -o read-plink.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c sp-colsumssq-sym.cpp -o sp-colsumssq-sym.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c split-LD.cpp -o split-LD.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/bigsparser/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/bigstatsr/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/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmio/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/roptim/include' -I/opt/R/x86_64/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -c write-plink.cpp -o write-plink.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 bigsnpr.so RcppExports.o bed-acc-xptr.o bed-fun.o bed-mat-acc.o bed-prod-vec.o clumping-bed.o clumping-cached.o clumping.o colstats.o copy-subset.o corr.o corr_with_cov.o impute-simple.o lassosum2.o ld-scores-sfbm.o ld-scores.o ldpred2-auto.o ldpred2-sampling.o ldpred2.o multLinReg.o prod-bgen.o project-utils.o read-bgen.o read-plink.o sp-colsumssq-sym.o split-LD.o write-plink.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 -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/Volumes/Builds/packages/big-sur-x86_64/results/4.4/bigsnpr.Rcheck/00_pkg_src/bigsnpr/src/corr_with_cov.o: no symbols
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/bigsnpr.Rcheck/00LOCK-bigsnpr/00new/bigsnpr/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** 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 (bigsnpr)