* installing *source* package 'MasterBayes' ...
** package 'MasterBayes' 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/2026_03_20_17_24_58_29830/RtmpKSKt5R/R.INSTALL175f443d4c8e/MasterBayes/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ErrorMat.cc -o ErrorMat.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LikFunctions.cc -o LikFunctions.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MCMCped.cc -o MCMCped.o
MCMCped.cc: In function 'void MCMCped(int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*)':
MCMCped.cc:942:11: warning: 'ppost_G' may be used uninitialized [-Wmaybe-uninitialized]
942 | delete [] ppost_G;
| ^~~~~~~
MCMCped.cc:139:10: note: 'ppost_G' was declared here
139 | *ppost_G,
| ^~~~~~~
MCMCped.cc:836:31: warning: 'post_G' may be used uninitialized [-Wmaybe-uninitialized]
836 | post_G[i][(l*3)+na1] ++;
| ~~~~~~~~^
MCMCped.cc:140:11: note: 'post_G' was declared here
140 | **post_G;
| ^~~~~~
gcc -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MasterBayes_init.c -o MasterBayes_init.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Read_in_data.cc -o Read_in_data.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampD.cc -o SampD.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampDomG.cc -o SampDomG.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampG.cc -o SampG.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampGC.cc -o SampGC.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampP.cc -o SampP.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampS.cc -o SampS.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpecRand.cc -o SpecRand.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcX_G.cc -o calcX_G.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcX_GD.cc -o calcX_GD.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcX_GS.cc -o calcX_GS.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcX_Gcervus.cc -o calcX_Gcervus.o
calcX_Gcervus.cc: In function 'void calcX_Gcervus(scythe::Matrix<>*, int*, int, int*, int*, int, scythe::Matrix<int>*, scythe::Matrix<int>*, int**, int, double**, double**, int, int*)':
calcX_Gcervus.cc:32:16: warning: variable 'q' set but not used [-Wunused-but-set-variable]
32 | double q;
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcX_GcervusD.cc -o calcX_GcervusD.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcX_GcervusS.cc -o calcX_GcervusS.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calcX_Gmm.cc -o calcX_Gmm.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fillXG.cc -o fillXG.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c legalG.cc -o legalG.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3p/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mismatches.cc -o mismatches.o
g++ -std=gnu++17 -shared -s -static-libgcc -o MasterBayes.dll tmp.def ErrorMat.o LikFunctions.o MCMCped.o MasterBayes_init.o Read_in_data.o SampD.o SampDomG.o SampG.o SampGC.o SampP.o SampS.o SpecRand.o calcX_G.o calcX_GD.o calcX_GS.o calcX_Gcervus.o calcX_GcervusD.o calcX_GcervusS.o calcX_Gmm.o fillXG.o legalG.o mismatches.o -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.3p/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2026_03_20_17_24_58_29830/RtmpKSKt5R/R.INSTALL175f443d4c8e/MasterBayes/src'
make[1]: Entering directory '/d/temp/2026_03_20_17_24_58_29830/RtmpKSKt5R/R.INSTALL175f443d4c8e/MasterBayes/src'
make[1]: Leaving directory '/d/temp/2026_03_20_17_24_58_29830/RtmpKSKt5R/R.INSTALL175f443d4c8e/MasterBayes/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-MasterBayes/00new/MasterBayes/libs/x64
** R
** data
** 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 'MasterBayes' as MasterBayes_2.59.zip
* DONE (MasterBayes)