Install log for 'bigstatsr'

* installing *source* package ‘bigstatsr’ ...
** package ‘bigstatsr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/bigstatsr/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c AUC.cpp -o AUC.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c FBM-extract.cpp -o FBM-extract.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c FBM-replace.cpp -o FBM-replace.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c FBM-xptr.cpp -o FBM-xptr.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c arma-prod-self-sub.cpp -o arma-prod-self-sub.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c arma-prod-sub.cpp -o arma-prod-sub.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c arma-prod.cpp -o arma-prod.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c biglassoLin.cpp -o biglassoLin.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c biglassoLog.cpp -o biglassoLog.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c biglassoUtils.cpp -o biglassoUtils.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c colstats.cpp -o colstats.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c counts.cpp -o counts.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c errorMsgs.cpp -o errorMsgs.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c prodMatVec.cpp -o prodMatVec.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c transpose.cpp -o transpose.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c univRegLin5.cpp -o univRegLin5.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c univRegLog.cpp -o univRegLog.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/rmio/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c utils-mat.cpp -o utils-mat.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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 -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/bigstatsr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/bigstatsr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/bigstatsr/src'
installing to /data/gannet/ripley/R/packages/tests-clang/bigstatsr.Rcheck/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
** 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 (bigstatsr)