* installing *source* package ‘AlphaSimR’ ...
** package ‘AlphaSimR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MME.cpp -o MME.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c algorithm.cpp -o algorithm.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c alphaSuite.cpp -o alphaSuite.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c altAddTraitAD.cpp -o altAddTraitAD.o
algorithm.cpp:324:7: warning: variable 'iIterations' set but not used [-Wunused-but-set-variable]
324 | int iIterations = 0;
| ^
algorithm.cpp:1223:7: warning: variable 'xovers' set but not used [-Wunused-but-set-variable]
1223 | int xovers=0,gcstarts=0,gcends=0;
| ^
algorithm.cpp:1223:16: warning: variable 'gcstarts' set but not used [-Wunused-but-set-variable]
1223 | int xovers=0,gcstarts=0,gcends=0;
| ^
algorithm.cpp:1223:27: warning: variable 'gcends' set but not used [-Wunused-but-set-variable]
1223 | int xovers=0,gcstarts=0,gcends=0;
| ^
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c calcGenParam.cpp -o calcGenParam.o
4 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c datastructures.cpp -o datastructures.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c getGeno.cpp -o getGeno.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c getGv.cpp -o getGv.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c getHybridGv.cpp -o getHybridGv.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ibd.cpp -o ibd.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c meiosis.cpp -o meiosis.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c misc.cpp -o misc.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c optimize.cpp -o optimize.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c packHaplo.cpp -o packHaplo.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c simulator.cpp -o simulator.o
simulator.cpp:172:15: warning: variable 'total' set but not used [-Wunused-but-set-variable]
172 | int total=0;
| ^
simulator.cpp:233:15: warning: variable 'total' set but not used [-Wunused-but-set-variable]
233 | int total=0;
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -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 -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)