* installing *source* package 'hsphase' ... ** this is package 'hsphase' version '3.0.0' ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 14.3.0' g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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 SwitchAdd.cpp: In function 'SEXPREC* switchAdd(SEXP, SEXP, SEXP)': SwitchAdd.cpp:15:9: warning: unused variable 'minLength' [-Wunused-variable] 15 | int minLength = as(minlength); | ^~~~~~~~~ g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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 >::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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/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 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 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 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. installing to d:/RCompile/CRANincoming/R-devel/lib/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 * DONE (hsphase)