* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘bigsnpr’ ...
** package ‘bigsnpr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmppe9x4a/R.INSTALL2730b05ad7ac4c/bigsnpr/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bed-acc-xptr.cpp -o bed-acc-xptr.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bed-fun.cpp -o bed-fun.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bed-mat-acc.cpp -o bed-mat-acc.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bed-prod-vec.cpp -o bed-prod-vec.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c clumping-bed.cpp -o clumping-bed.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c clumping-cached.cpp -o clumping-cached.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c clumping.cpp -o clumping.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c colstats.cpp -o colstats.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c copy-subset.cpp -o copy-subset.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c corr.cpp -o corr.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c corr_with_cov.cpp -o corr_with_cov.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c impute-simple.cpp -o impute-simple.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c lassosum2.cpp -o lassosum2.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ld-scores-sfbm.cpp -o ld-scores-sfbm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ld-scores.cpp -o ld-scores.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ldpred2-auto.cpp -o ldpred2-auto.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ldpred2-sampling.cpp -o ldpred2-sampling.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ldpred2.cpp -o ldpred2.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c multLinReg.cpp -o multLinReg.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c prod-bgen.cpp -o prod-bgen.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c read-bgen.cpp -o read-bgen.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c read-plink.cpp -o read-plink.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sp-colsumssq-sym.cpp -o sp-colsumssq-sym.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c split-LD.cpp -o split-LD.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigsparser/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/bigstatsr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native   -c write-plink.cpp -o write-plink.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -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 read-bgen.o read-plink.o sp-colsumssq-sym.o split-LD.o write-plink.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmppe9x4a/R.INSTALL2730b05ad7ac4c/bigsnpr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmppe9x4a/R.INSTALL2730b05ad7ac4c/bigsnpr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmppe9x4a/R.INSTALL2730b05ad7ac4c/bigsnpr/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-bigsnpr/00new/bigsnpr/libs
** 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
* creating tarball
packaged installation of ‘bigsnpr’ as ‘bigsnpr_1.12.2_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (bigsnpr)