Install log for 'MasterBayes'

* installing to library ‘/home/hornik/tmp/R.check/r-release-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 15.2.0-14) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbVn43s/R.INSTALL1b30eb502a2764/MasterBayes/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbVn43s/R.INSTALL1b30eb502a2764/MasterBayes/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbVn43s/R.INSTALL1b30eb502a2764/MasterBayes/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbVn43s/R.INSTALL1b30eb502a2764/MasterBayes/src'
installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-MasterBayes/00new/MasterBayes/libs
** 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
** 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)