* 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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/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/4.3/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)