* installing *source* package 'hsphase' ...
** this is package 'hsphase' version '3.0.1'
** package 'hsphase' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 14.3.0'
make[1]: Entering directory '/d/temp/2026_07_17_01_50_00_19668/RtmpC6A0PW/R.INSTALL116402e357ff/hsphase/src'
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastDist.cpp -o FastDist.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FillGap.cpp -o FillGap.o
FillGap.cpp: In function 'int fillGapFunction(int*, int*, int*)':
FillGap.cpp:24:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
24 | for (size_t j = 0; j < *length; j++)
| ~~^~~~~~~~~
FillGap.cpp:33:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
33 | for (size_t j = 0; j < gapLength; j++)
| ~~^~~~~~~~~~~
FillGap.cpp:51:56: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
51 | for (size_t j = *length - 1; j > (*length-gapLength - 1); j--)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
FillGap.cpp:72:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
72 | for (size_t j = i; j < (*length - 1); j++)
| ~~^~~~~~~~~~~~~~~
FillGap.cpp:81:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
81 | for (size_t j = i; j < i + (gapLength / 2); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~
FillGap.cpp:87:64: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
87 | for (size_t j = i + (gapLength / 2); j < i + gapLength; j++)
| ~~^~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FixBothStrand.cpp -o FixBothStrand.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MAF.cpp -o MAF.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Ohd.cpp -o Ohd.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SwitchAdd.cpp -o SwitchAdd.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SwitchDetector.cpp -o SwitchDetector.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TypeConversion.cpp -o TypeConversion.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c block.cpp -o block.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c block4Phase.cpp -o block4Phase.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c co.cpp -o co.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c diag.cpp -o diag.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fixRotation.cpp -o fixRotation.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hsp.cpp -o hsp.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ibdcluster.cpp -o ibdcluster.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c memory.cpp -o memory.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mhMat.cpp -o mhMat.o
mhMat.cpp: In member function 'void mhMat::keep2MostFrequent()':
mhMat.cpp:102:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
102 | for (int j = 0; j < groupResult.size(); ++j)
| ~~^~~~~~~~~~~~~~~~~~~~
mhMat.cpp:146:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
146 | if (*it != itr->second && *it != itr2->second)
| ~~~~^~~~~~~~~~~~~~
mhMat.cpp:146:63: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
146 | if (*it != itr->second && *it != itr2->second)
| ~~~~^~~~~~~~~~~~~~~
mhMat.cpp:150:46: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
150 | else if (*it == itr->second)
| ~~~~^~~~~~~~~~~~~~
mhMat.cpp:154:46: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
154 | else if (*it == itr2->second)
| ~~~~^~~~~~~~~~~~~~~
mhMat.cpp:161:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
161 | if (*it != itr->second)
| ~~~~^~~~~~~~~~~~~~
mhMat.cpp:165:46: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
165 | else if (*it == itr->second)
| ~~~~^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c oh.cpp -o oh.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ohg.cpp -o ohg.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ohp.cpp -o ohp.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c swDetect.cpp -o swDetect.o
g++ -std=gnu++20 -shared -s -static-libgcc -o hsphase.dll tmp.def FastDist.o FillGap.o FixBothStrand.o MAF.o Ohd.o SwitchAdd.o SwitchDetector.o TypeConversion.o block.o block4Phase.o co.o diag.o fixRotation.o hsp.o ibdcluster.o main.o memory.o mhMat.o oh.o ohg.o ohp.o swDetect.o -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lquadmath -fopenmp -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2026_07_17_01_50_00_19668/RtmpC6A0PW/R.INSTALL116402e357ff/hsphase/src'
make[1]: Entering directory '/d/temp/2026_07_17_01_50_00_19668/RtmpC6A0PW/R.INSTALL116402e357ff/hsphase/src'
make[1]: Leaving directory '/d/temp/2026_07_17_01_50_00_19668/RtmpC6A0PW/R.INSTALL116402e357ff/hsphase/src'
installing to d:/Rcompile/CRANpkg/lib/4.7/00LOCK-hsphase/00new/hsphase/libs/x64
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 'hsphase' as hsphase_3.0.1.zip
* DONE (hsphase)