* 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 15.2.0-17) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-17) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3GsBmy/R.INSTALL236ef566d4b216/MasterBayes/src' g++-15 -std=gnu++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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*, scythe::Matrix*, 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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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/Rtmp3GsBmy/R.INSTALL236ef566d4b216/MasterBayes/src' make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3GsBmy/R.INSTALL236ef566d4b216/MasterBayes/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3GsBmy/R.INSTALL236ef566d4b216/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)