* installing *source* package 'mvMAPIT' ...
** package 'mvMAPIT' 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_08_01_50_01_8405/RtmpSIEz56/R.INSTALL892820b41c62/mvMAPIT/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MAPIT.cpp -o MAPIT.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -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 -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gsm/gsm.cpp -o gsm/gsm.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logging/log.cpp -o logging/log.o
logging/log.cpp: In function 'std::string phenotype_vector_to_string(const std::vector<arma::Col<double> >&)':
logging/log.cpp:6:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<arma::Col<double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
6 | for (int i = 1; i < v.size(); i++) {
| ~~^~~~~~~~~~
logging/log.cpp: In function 'std::string vector_to_string(const arma::vec&)':
logging/log.cpp:15:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
15 | for (int i = 1; i < v.n_elem; i++) {
| ~~^~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mapit/davies.cpp -o mapit/davies.o
mapit/davies.cpp: In function 'arma::mat davies_routine(const arma::mat&, const arma::mat&, const arma::mat&, const std::vector<arma::Mat<double> >&)':
mapit/davies.cpp:16:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
16 | for (int i = 0; i < q.n_cols; i++) {
| ~~^~~~~~~~~~
mapit/davies.cpp: In function 'arma::vec davies_routine_vec(const arma::mat&, const arma::mat&, const arma::vec&, const std::vector<arma::Mat<double> >&)':
mapit/davies.cpp:36:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
36 | for (int i = 0; i < q_sub.n_elem; i++) {
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mapit/normal.cpp -o mapit/normal.o
mapit/normal.cpp: In function 'arma::mat normal_pvalues(const arma::mat&, const arma::mat&)':
mapit/normal.cpp:23:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
23 | for (int j = 0; j < variance_estimate.n_cols; j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
mapit/normal.cpp:24:23: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
24 | for (int i = 0; i < variance_estimate.n_rows; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mapit/projection.cpp -o mapit/projection.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mapit/pve.cpp -o mapit/pve.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mapit/util.cpp -o mapit/util.o
mapit/util.cpp: In function 'arma::vec remove_first_element(const arma::vec&)':
mapit/util.cpp:17:21: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'long long unsigned int'} [-Wsign-compare]
17 | for (int i = 1; i < vector.size(); i++) {
| ~~^~~~~~~~~~~~~~~
mapit/util.cpp: In function 'std::vector<arma::Col<double> > matrix_to_vector_of_rows(const arma::mat&)':
mapit/util.cpp:37:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
37 | for (int i = 0; i < matrix.n_rows; ++i) {
| ~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mqs/mqs.cpp -o mqs/mqs.o
mqs/mqs.cpp: In function 'arma::mat compute_h_matrix(const arma::mat&, const std::vector<arma::Mat<double> >&)':
mqs/mqs.cpp:113:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<arma::Mat<double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
113 | for (int i = 0; i < matrices.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
mqs/mqs.cpp: In function 'arma::mat compute_v_matrix(const arma::vec&, const std::vector<arma::Mat<double> >&)':
mqs/mqs.cpp:129:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<arma::Mat<double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
129 | for (int i = 0; i < matrices.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
mqs/mqs.cpp: In function 'arma::vec compute_variance_delta(const std::vector<arma::Col<double> >&, const arma::mat&, const arma::mat&, const std::vector<arma::Mat<double> >&)':
mqs/mqs.cpp:171:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare]
171 | for (int k = 0; k < delta.n_cols; k++) {
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-compare-to-original-mapit.cpp -o tests/test-compare-to-original-mapit.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-davies.cpp -o tests/test-davies.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-gsm.cpp -o tests/test-gsm.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-log.cpp -o tests/test-log.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-mqs.cpp -o tests/test-mqs.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-normal.cpp -o tests/test-normal.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-projection.cpp -o tests/test-projection.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-pve.cpp -o tests/test-pve.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-runner.cpp -o tests/test-runner.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -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/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppSpdlog/include' -I'D:/RCompile/CRANpkg/lib/4.4/testthat/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tests/test-util.cpp -o tests/test-util.o
g++ -std=gnu++17 -shared -s -static-libgcc -o mvMAPIT.dll tmp.def MAPIT.o RcppExports.o gsm/gsm.o logging/log.o mapit/davies.o mapit/normal.o mapit/projection.o mapit/pve.o mapit/util.o mqs/mqs.o tests/test-compare-to-original-mapit.o tests/test-davies.o tests/test-gsm.o tests/test-log.o tests/test-mqs.o tests/test-normal.o tests/test-projection.o tests/test-pve.o tests/test-runner.o tests/test-util.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_08_01_50_01_8405/RtmpSIEz56/R.INSTALL892820b41c62/mvMAPIT/src'
make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpSIEz56/R.INSTALL892820b41c62/mvMAPIT/src'
make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/RtmpSIEz56/R.INSTALL892820b41c62/mvMAPIT/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-mvMAPIT/00new/mvMAPIT/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 'mvMAPIT' as mvMAPIT_2.0.3.zip
* DONE (mvMAPIT)