* installing *source* package ‘statgenIBD’ ...
** package ‘statgenIBD’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.sdk’
rm -f calcIBD.o RcppExports.o general/HMMalgo.o general/InhVector.o general/ibdexcept.o general/misc.o general/OrdGeno.o general/TransMatSym2D.o general/util_genetics.o pedigree/analysis_fam.o pedigree/crosses.o pedigree/Loc.o pedigree/mainR.o pedigree/markerscore.o pedigree/popt.o pedigree/read_map.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calcIBD.cpp -o calcIBD.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general/HMMalgo.cpp -o general/HMMalgo.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general/InhVector.cpp -o general/InhVector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general/ibdexcept.cpp -o general/ibdexcept.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general/misc.cpp -o general/misc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general/OrdGeno.cpp -o general/OrdGeno.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general/TransMatSym2D.cpp -o general/TransMatSym2D.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general/util_genetics.cpp -o general/util_genetics.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree/analysis_fam.cpp -o pedigree/analysis_fam.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree/crosses.cpp -o pedigree/crosses.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree/Loc.cpp -o pedigree/Loc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree/mainR.cpp -o pedigree/mainR.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree/markerscore.cpp -o pedigree/markerscore.o
calcIBD.cpp:109:19: warning: unused variable 'popt' [-Wunused-variable]
const pop_base *popt = init_pop(_poptype);
^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree/popt.cpp -o pedigree/popt.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Igeneral -Ipedigree -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree/read_map.cpp -o pedigree/read_map.o
1 warning generated.
pedigree/mainR.cpp:209:7: warning: variable 'Nfnd' set but not used [-Wunused-but-set-variable]
int Nfnd = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o statgenIBD.so calcIBD.o RcppExports.o general/HMMalgo.o general/InhVector.o general/ibdexcept.o general/misc.o general/OrdGeno.o general/TransMatSym2D.o general/util_genetics.o pedigree/analysis_fam.o pedigree/crosses.o pedigree/Loc.o pedigree/mainR.o pedigree/markerscore.o pedigree/popt.o pedigree/read_map.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/statgenIBD.Rcheck/00LOCK-statgenIBD/00new/statgenIBD/libs
** generating debug symbols (dSYM)
** 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 (statgenIBD)