* installing *source* package ‘AlphaSimR’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 16.0.6 (16)’ clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c MME.cpp -o MME.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c algorithm.cpp -o algorithm.o algorithm.cpp:324:7: warning: variable 'iIterations' set but not used [-Wunused-but-set-variable] int iIterations = 0; ^ algorithm.cpp:1223:7: warning: variable 'xovers' set but not used [-Wunused-but-set-variable] int xovers=0,gcstarts=0,gcends=0; ^ algorithm.cpp:1223:16: warning: variable 'gcstarts' set but not used [-Wunused-but-set-variable] int xovers=0,gcstarts=0,gcends=0; ^ algorithm.cpp:1223:27: warning: variable 'gcends' set but not used [-Wunused-but-set-variable] int xovers=0,gcstarts=0,gcends=0; ^ 4 warnings generated. clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c alphaSuite.cpp -o alphaSuite.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c altAddTraitAD.cpp -o altAddTraitAD.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c calcGenParam.cpp -o calcGenParam.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c datastructures.cpp -o datastructures.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c getGeno.cpp -o getGeno.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c getGv.cpp -o getGv.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c getHybridGv.cpp -o getHybridGv.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c ibd.cpp -o ibd.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c meiosis.cpp -o meiosis.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c misc.cpp -o misc.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c optimize.cpp -o optimize.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c packHaplo.cpp -o packHaplo.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -g -O3 -Wall -pedantic -c simulator.cpp -o simulator.o simulator.cpp:172:15: warning: variable 'total' set but not used [-Wunused-but-set-variable] int total=0; ^ simulator.cpp:233:15: warning: variable 'total' set but not used [-Wunused-but-set-variable] int total=0; ^ 2 warnings generated. clang++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-16/lib -Wl,-O1 -o AlphaSimR.so MME.o RcppExports.o algorithm.o alphaSuite.o altAddTraitAD.o calcGenParam.o datastructures.o getGeno.o getGv.o getHybridGv.o ibd.o meiosis.o misc.o optimize.o packHaplo.o simulator.o -llapack -L/home/hornik/tmp/R-d-clang-16/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R-d-clang-16/lib -lR installing to /srv/hornik/tmp/CRAN/AlphaSimR.Rcheck/00LOCK-AlphaSimR/00new/AlphaSimR/libs ** 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 ** 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 (AlphaSimR)