* installing *source* package 'Morpho' ...
** package 'Morpho' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/Rtmp48vOYO/R.INSTALL30d3431c24a2/Morpho/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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CVAdists.cpp -o CVAdists.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CubeStuff.cpp -o CubeStuff.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ang_calc.cpp -o ang_calc.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c armaGinvCpp.cpp -o armaGinvCpp.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c asymPerm.cpp -o asymPerm.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c barycenter.cpp -o barycenter.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c covPCA.cpp -o covPCA.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c createL.cpp -o createL.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doozers.cpp -o doozers.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c edgePlane.cpp -o edgePlane.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c face_zero.cpp -o face_zero.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastSubsetMeans.cpp -o fastSubsetMeans.o
fastSubsetMeans.cpp: In function 'SEXPREC* fastSubsetMeans(SEXP, SEXP, SEXP, SEXP)':
fastSubsetMeans.cpp:22:25: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
22 | for (int j = 0; j < tmpinds.size();j++)
| ~~^~~~~~~~~~~~~~~~
gcc -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:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c meshres.cpp -o meshres.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c permudistArma.cpp -o permudistArma.o
permudistArma.cpp: In function 'SEXPREC* permudistArma(SEXP, SEXP, SEXP, SEXP)':
permudistArma.cpp:9:10: warning: unused variable 'usemedian' [-Wunused-variable]
9 | bool usemedian = Rcpp::as<bool>(usemedian_);
| ^~~~~~~~~
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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c points2mesh.cpp -o points2mesh.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tpsfx.cpp -o tpsfx.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tweakU.cpp -o tweakU.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:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updateNormals.cpp -o updateNormals.o
g++ -std=gnu++17 -shared -s -static-libgcc -o Morpho.dll tmp.def CVAdists.o CubeStuff.o ang_calc.o armaGinvCpp.o asymPerm.o barycenter.o covPCA.o createL.o doozers.o edgePlane.o face_zero.o fastSubsetMeans.o init.o meshres.o permudistArma.o points2mesh.o tpsfx.o tweakU.o updateNormals.o -LD:/RCompile/recent/R-4.4.2/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.4.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -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/Rtmp48vOYO/R.INSTALL30d3431c24a2/Morpho/src'
make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/Rtmp48vOYO/R.INSTALL30d3431c24a2/Morpho/src'
make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/Rtmp48vOYO/R.INSTALL30d3431c24a2/Morpho/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-Morpho/00new/Morpho/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 'Morpho' as Morpho_2.12.zip
* DONE (Morpho)