* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘AlphaSimR’ ...
** package ‘AlphaSimR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 19.1.6 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgLv9C9/R.INSTALL224c773b59aa85/AlphaSimR/src'
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c MME.cpp -o MME.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c algorithm.cpp -o algorithm.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c alphaSuite.cpp -o alphaSuite.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c altAddTraitAD.cpp -o altAddTraitAD.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c calcGenParam.cpp -o calcGenParam.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c datastructures.cpp -o datastructures.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c getGeno.cpp -o getGeno.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c getGv.cpp -o getGv.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c getHybridGv.cpp -o getHybridGv.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c ibd.cpp -o ibd.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c meiosis.cpp -o meiosis.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c misc.cpp -o misc.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c optimize.cpp -o optimize.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c packHaplo.cpp -o packHaplo.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c simulator.cpp -o simulator.o
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/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.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgLv9C9/R.INSTALL224c773b59aa85/AlphaSimR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgLv9C9/R.INSTALL224c773b59aa85/AlphaSimR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgLv9C9/R.INSTALL224c773b59aa85/AlphaSimR/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)