* installing *source* package 'bigstatsr' ...
** package 'bigstatsr' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2024_12_21_01_50_00_6285/RtmpuqoRfb/R.INSTALL9cc451456625/bigstatsr/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AUC.cpp -o AUC.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FBM-extract.cpp -o FBM-extract.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FBM-replace.cpp -o FBM-replace.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FBM-xptr.cpp -o FBM-xptr.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c arma-prod-self-sub.cpp -o arma-prod-self-sub.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c arma-prod-sub.cpp -o arma-prod-sub.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c arma-prod.cpp -o arma-prod.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biglassoLin.cpp -o biglassoLin.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biglassoLog.cpp -o biglassoLog.o
In file included from biglassoLog.cpp:4:
../inst/include/bigstatsr/biglasso/logistic.hpp: In function 'Rcpp::List bigstatsr::biglassoLog::COPY_cdfit_binomial_hsr(C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, Rcpp::NumericVector&, double, double, int, int, C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int) [with C = RawSubMatCovAcc]':
../inst/include/bigstatsr/biglasso/logistic.hpp:212:41: warning: 'sum_s' may be used uninitialized [-Wmaybe-uninitialized]
212 | violations = COPY_check_strong_set(
| ~~~~~~~~~~~~~~~~~~~~~^
213 | in_A, in_S, z, macc, center, scale, pf, beta_old, l1, l2, s, sum_s);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp:76:21: note: 'sum_s' was declared here
76 | double sumWResid, sum_s, sum_wx_sq, sum_wx, sum_w, x, xw;
| ^~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp: In function 'Rcpp::List bigstatsr::biglassoLog::COPY_cdfit_binomial_hsr(C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, Rcpp::NumericVector&, double, double, int, int, C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int) [with C = SubMatCovAcc<double>]':
../inst/include/bigstatsr/biglasso/logistic.hpp:212:41: warning: 'sum_s' may be used uninitialized [-Wmaybe-uninitialized]
212 | violations = COPY_check_strong_set(
| ~~~~~~~~~~~~~~~~~~~~~^
213 | in_A, in_S, z, macc, center, scale, pf, beta_old, l1, l2, s, sum_s);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp:76:21: note: 'sum_s' was declared here
76 | double sumWResid, sum_s, sum_wx_sq, sum_wx, sum_w, x, xw;
| ^~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp: In function 'Rcpp::List bigstatsr::biglassoLog::COPY_cdfit_binomial_hsr(C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, Rcpp::NumericVector&, double, double, int, int, C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int) [with C = SubMatCovAcc<int>]':
../inst/include/bigstatsr/biglasso/logistic.hpp:212:41: warning: 'sum_s' may be used uninitialized [-Wmaybe-uninitialized]
212 | violations = COPY_check_strong_set(
| ~~~~~~~~~~~~~~~~~~~~~^
213 | in_A, in_S, z, macc, center, scale, pf, beta_old, l1, l2, s, sum_s);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp:76:21: note: 'sum_s' was declared here
76 | double sumWResid, sum_s, sum_wx_sq, sum_wx, sum_w, x, xw;
| ^~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp: In function 'Rcpp::List bigstatsr::biglassoLog::COPY_cdfit_binomial_hsr(C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, Rcpp::NumericVector&, double, double, int, int, C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int) [with C = SubMatCovAcc<float>]':
../inst/include/bigstatsr/biglasso/logistic.hpp:212:41: warning: 'sum_s' may be used uninitialized [-Wmaybe-uninitialized]
212 | violations = COPY_check_strong_set(
| ~~~~~~~~~~~~~~~~~~~~~^
213 | in_A, in_S, z, macc, center, scale, pf, beta_old, l1, l2, s, sum_s);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp:76:21: note: 'sum_s' was declared here
76 | double sumWResid, sum_s, sum_wx_sq, sum_wx, sum_w, x, xw;
| ^~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp: In function 'Rcpp::List bigstatsr::biglassoLog::COPY_cdfit_binomial_hsr(C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, Rcpp::NumericVector&, double, double, int, int, C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int) [with C = SubMatCovAcc<unsigned char>]':
../inst/include/bigstatsr/biglasso/logistic.hpp:212:41: warning: 'sum_s' may be used uninitialized [-Wmaybe-uninitialized]
212 | violations = COPY_check_strong_set(
| ~~~~~~~~~~~~~~~~~~~~~^
213 | in_A, in_S, z, macc, center, scale, pf, beta_old, l1, l2, s, sum_s);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp:76:21: note: 'sum_s' was declared here
76 | double sumWResid, sum_s, sum_wx_sq, sum_wx, sum_w, x, xw;
| ^~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp: In function 'Rcpp::List bigstatsr::biglassoLog::COPY_cdfit_binomial_hsr(C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, Rcpp::NumericVector&, double, double, int, int, C, const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int) [with C = SubMatCovAcc<short unsigned int>]':
../inst/include/bigstatsr/biglasso/logistic.hpp:212:41: warning: 'sum_s' may be used uninitialized [-Wmaybe-uninitialized]
212 | violations = COPY_check_strong_set(
| ~~~~~~~~~~~~~~~~~~~~~^
213 | in_A, in_S, z, macc, center, scale, pf, beta_old, l1, l2, s, sum_s);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../inst/include/bigstatsr/biglasso/logistic.hpp:76:21: note: 'sum_s' was declared here
76 | double sumWResid, sum_s, sum_wx_sq, sum_wx, sum_w, x, xw;
| ^~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biglassoUtils.cpp -o biglassoUtils.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c colstats.cpp -o colstats.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c counts.cpp -o counts.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c errorMsgs.cpp -o errorMsgs.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c prodMatVec.cpp -o prodMatVec.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transpose.cpp -o transpose.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c univRegLin5.cpp -o univRegLin5.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c univRegLog.cpp -o univRegLog.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/rmio/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -fopenmp -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -DARMA_64BIT_WORD=1 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils-mat.cpp -o utils-mat.o
g++ -std=gnu++17 -shared -s -static-libgcc -o bigstatsr.dll tmp.def 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 -LD:/RCompile/recent/R-4.4.2/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.4.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_21_01_50_00_6285/RtmpuqoRfb/R.INSTALL9cc451456625/bigstatsr/src'
make[1]: Entering directory '/d/temp/2024_12_21_01_50_00_6285/RtmpuqoRfb/R.INSTALL9cc451456625/bigstatsr/src'
make[1]: Leaving directory '/d/temp/2024_12_21_01_50_00_6285/RtmpuqoRfb/R.INSTALL9cc451456625/bigstatsr/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-bigstatsr/00new/bigstatsr/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'bigstatsr' as bigstatsr_1.6.1.zip
* DONE (bigstatsr)