* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘MasterBayes’ ...
** this is package ‘MasterBayes’ version ‘2.59’
** package ‘MasterBayes’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-15) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFMkphW/R.INSTALL259c0c17ac46/MasterBayes/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ErrorMat.cc -o ErrorMat.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c LikFunctions.cc -o LikFunctions.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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-15 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c MasterBayes_init.c -o MasterBayes_init.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Read_in_data.cc -o Read_in_data.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SampD.cc -o SampD.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SampDomG.cc -o SampDomG.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SampG.cc -o SampG.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SampGC.cc -o SampGC.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SampP.cc -o SampP.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SampS.cc -o SampS.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SpecRand.cc -o SpecRand.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcX_G.cc -o calcX_G.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcX_GD.cc -o calcX_GD.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcX_GS.cc -o calcX_GS.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcX_GcervusD.cc -o calcX_GcervusD.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcX_GcervusS.cc -o calcX_GcervusS.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calcX_Gmm.cc -o calcX_Gmm.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fillXG.cc -o fillXG.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c legalG.cc -o legalG.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mismatches.cc -o mismatches.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o MasterBayes.so 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 -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFMkphW/R.INSTALL259c0c17ac46/MasterBayes/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFMkphW/R.INSTALL259c0c17ac46/MasterBayes/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFMkphW/R.INSTALL259c0c17ac46/MasterBayes/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-MasterBayes/00new/MasterBayes/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘MasterBayes’
finding HTML links ... done
GdataPed html
MCMCped html
MLE.beta html
MLE.ped html
MLE.popsize html
MasterBayes html
PdataPed html
WarblerG html
WarblerP html
autocorrP html
beta.loglik html
consenusG html
extractA html
fillX.G html
genotype.list html
genotypeD html
getXlist html
insertPed html
legalG html
mismatches html
modeG html
modeP html
orderPed html
popsize.loglik html
post.pairs html
priorPed html
reordXlist html
simgenotypes html
simpedigree html
startPed html
summary.genotypeD html
tunePed html
varPed html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MasterBayes)