* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘bigstatsr’ ...
** package ‘bigstatsr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmplVo1uw/R.INSTALL1d26e75c5f43e4/bigstatsr/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c AUC.cpp -o AUC.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c FBM-extract.cpp -o FBM-extract.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c FBM-replace.cpp -o FBM-replace.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c FBM-xptr.cpp -o FBM-xptr.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -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++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c arma-prod-self-sub.cpp -o arma-prod-self-sub.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c arma-prod-sub.cpp -o arma-prod-sub.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c arma-prod.cpp -o arma-prod.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c biglassoLin.cpp -o biglassoLin.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c biglassoLog.cpp -o biglassoLog.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c biglassoUtils.cpp -o biglassoUtils.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -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++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c counts.cpp -o counts.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c errorMsgs.cpp -o errorMsgs.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c prodMatVec.cpp -o prodMatVec.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c transpose.cpp -o transpose.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c univRegLin5.cpp -o univRegLin5.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c univRegLog.cpp -o univRegLog.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils-mat.cpp -o utils-mat.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o bigstatsr.so AUC.o FBM-extract.o FBM-replace.o FBM-xptr.o RcppExports.o arma-prod-self-sub.o arma-prod-sub.o arma-prod.o biglassoLin.o biglassoLog.o biglassoUtils.o colstats.o counts.o errorMsgs.o prodMatVec.o transpose.o univRegLin5.o univRegLog.o utils-mat.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmplVo1uw/R.INSTALL1d26e75c5f43e4/bigstatsr/src'
make[1]: Entering directory '/tmp/RtmplVo1uw/R.INSTALL1d26e75c5f43e4/bigstatsr/src'
make[1]: Leaving directory '/tmp/RtmplVo1uw/R.INSTALL1d26e75c5f43e4/bigstatsr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bigstatsr/00new/bigstatsr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘typeof’ from package ‘base’ in package ‘bigstatsr’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘bigstatsr’
** help
*** installing help indices
converting help for package ‘bigstatsr’
finding HTML links ... done
AUC html
COPY_biglasso_main html
COPY_biglasso_part html
Extract html
FBM-class html
FBM-methods html
FBM.code256-class html
Replace html
asPlotlyText html
as_scaling_fun html
big_SVD html
big_apply html
big_attach html
big_colstats html
big_copy html
big_cor html
big_counts html
big_cprodMat html
big_cprodVec html
big_crossprodSelf html
big_increment html
big_parallelize html
big_prodMat html
big_prodVec html
big_randomSVD html
big_read html
big_scale html
big_spLinReg html
big_spLogReg html
big_tcrossprodSelf html
big_transpose html
big_univLinReg html
big_univLogReg html
big_write html
bigstatsr-package html
block_size html
covar_from_df html
get_beta html
pasteLoc html
pcor html
plot.big_SVD html
plot.big_sp_list html
plot.mhtest html
predict.big_SVD html
predict.big_sp html
predict.big_sp_list html
predict.mhtest html
reexports html
sub_bk html
summary.big_sp_list html
theme_bigstatsr html
without_downcast_warning html
** 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 ‘bigstatsr’ as ‘bigstatsr_1.5.12_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (bigstatsr)