* 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" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastDist.cpp -o FastDist.o FastDist.cpp:47: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 47 | #pragma omp parallel for private(frq) schedule(dynamic) 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" -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" -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" -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" -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" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SwitchAdd.cpp -o SwitchAdd.o SwitchAdd.cpp:35: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 35 | #pragma omp parallel for 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" -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" -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" -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" -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" -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" -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" -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" -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" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ibdcluster.cpp -o ibdcluster.o ibdcluster.cpp:31: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 31 | #pragma omp parallel for 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" -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" -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" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mhMat.cpp -o mhMat.o mhMat.cpp: In member function 'void mhMat::ohSimplify(int)': mhMat.cpp:34:14: error: 'uint' was not declared in this scope; did you mean 'rint'? 34 | for (uint j = 0; j < ohMat.n_cols; j++) | ^~~~ | rint mhMat.cpp:34:36: error: use of 'this' in a constant expression 34 | for (uint j = 0; j < ohMat.n_cols; j++) | ^~~~~~ mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:36: error: use of 'this' in a constant expression mhMat.cpp:34:26: error: 'j' was not declared in this scope; did you mean 'jn'? 34 | for (uint j = 0; j < ohMat.n_cols; j++) | ^ | jn mhMat.cpp:36:26: error: expected ';' before 'i' 36 | for (uint i = 0; i < ohMat.n_rows; i++) | ^~ | ; mhMat.cpp:36:44: error: use of 'this' in a constant expression 36 | for (uint i = 0; i < ohMat.n_rows; i++) | ^~~~~~ mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:44: error: use of 'this' in a constant expression mhMat.cpp:36:34: error: 'i' was not declared in this scope 36 | for (uint i = 0; i < ohMat.n_rows; i++) | ^ mhMat.cpp: In member function 'void mhMat::validateohSimplify()': mhMat.cpp:66:14: error: 'uint' was not declared in this scope; did you mean 'rint'? 66 | for (uint j = 0; j < ohMat.n_cols; j++) | ^~~~ | rint mhMat.cpp:66:36: error: use of 'this' in a constant expression 66 | for (uint j = 0; j < ohMat.n_cols; j++) | ^~~~~~ mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:36: error: use of 'this' in a constant expression mhMat.cpp:66:26: error: 'j' was not declared in this scope; did you mean 'jn'? 66 | for (uint j = 0; j < ohMat.n_cols; j++) | ^ | jn mhMat.cpp:68:26: error: expected ';' before 'i' 68 | for (uint i = 0; i < ohMat.n_rows; i++) | ^~ | ; mhMat.cpp:68:44: error: use of 'this' in a constant expression 68 | for (uint i = 0; i < ohMat.n_rows; i++) | ^~~~~~ mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:44: error: use of 'this' in a constant expression mhMat.cpp:68:34: error: 'i' was not declared in this scope 68 | for (uint i = 0; i < ohMat.n_rows; i++) | ^ mhMat.cpp:93:14: error: 'uint' was not declared in this scope; did you mean 'rint'? 93 | for (uint i = 0; i < ohMat.n_rows; i++) | ^~~~ | rint mhMat.cpp:93:36: error: use of 'this' in a constant expression 93 | for (uint i = 0; i < ohMat.n_rows; i++) | ^~~~~~ mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:36: error: use of 'this' in a constant expression mhMat.cpp:93:26: error: 'i' was not declared in this scope 93 | for (uint i = 0; i < ohMat.n_rows; i++) | ^ 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) | ~~~~^~~~~~~~~~~~~~ make: *** [D:/RCompile/recent/R/etc/x64/Makeconf:304: mhMat.o] Error 1 ERROR: compilation failed for package 'hsphase' * removing 'd:/RCompile/CRANincoming/R-devel/lib/hsphase'