* installing *source* package 'statgenIBD' ...
** package 'statgenIBD' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 12.3.0'
make[1]: Entering directory '/d/temp/2024_12_20_01_50_00_19051/RtmpuSCIFa/R.INSTALL5fcc832f22/statgenIBD/src'
rm -f calcIBD.o RcppExports.o general/HMMalgo.o general/InhVector.o general/ibdexcept.o general/misc.o general/OrdGeno.o general/TransMatSym2D.o general/util_genetics.o pedigree/analysis_fam.o pedigree/crosses.o pedigree/Loc.o pedigree/mainR.o pedigree/markerscore.o pedigree/popt.o pedigree/read_map.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcIBD.cpp -o calcIBD.o
calcIBD.cpp: In function 'Rcpp::List calcIBD(Rcpp::CharacterVector&, Rcpp::CharacterVector&, Rcpp::CharacterVector&, Rcpp::Nullable<Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>&>, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage>&>, const bool&, const bool&)':
calcIBD.cpp:109:19: warning: unused variable 'popt' [-Wunused-variable]
109 | const pop_base *popt = init_pop(_poptype);
| ^~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general/HMMalgo.cpp -o general/HMMalgo.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general/InhVector.cpp -o general/InhVector.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general/ibdexcept.cpp -o general/ibdexcept.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general/misc.cpp -o general/misc.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general/OrdGeno.cpp -o general/OrdGeno.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general/TransMatSym2D.cpp -o general/TransMatSym2D.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general/util_genetics.cpp -o general/util_genetics.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedigree/analysis_fam.cpp -o pedigree/analysis_fam.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedigree/crosses.cpp -o pedigree/crosses.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedigree/Loc.cpp -o pedigree/Loc.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedigree/mainR.cpp -o pedigree/mainR.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedigree/markerscore.cpp -o pedigree/markerscore.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedigree/popt.cpp -o pedigree/popt.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedigree/read_map.cpp -o pedigree/read_map.o
g++ -std=gnu++17 -shared -s -static-libgcc -o statgenIBD.dll tmp.def calcIBD.o RcppExports.o general/HMMalgo.o general/InhVector.o general/ibdexcept.o general/misc.o general/OrdGeno.o general/TransMatSym2D.o general/util_genetics.o pedigree/analysis_fam.o pedigree/crosses.o pedigree/Loc.o pedigree/mainR.o pedigree/markerscore.o pedigree/popt.o pedigree/read_map.o -LD:/RCompile/recent/R-4.3.3/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.3.3/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_20_01_50_00_19051/RtmpuSCIFa/R.INSTALL5fcc832f22/statgenIBD/src'
make[1]: Entering directory '/d/temp/2024_12_20_01_50_00_19051/RtmpuSCIFa/R.INSTALL5fcc832f22/statgenIBD/src'
make[1]: Leaving directory '/d/temp/2024_12_20_01_50_00_19051/RtmpuSCIFa/R.INSTALL5fcc832f22/statgenIBD/src'
installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-statgenIBD/00new/statgenIBD/libs/x64
** R
** 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 'statgenIBD' as statgenIBD_1.0.7.zip
* DONE (statgenIBD)