############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneticsPed ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘GeneticsPed’ ... ** this is package ‘GeneticsPed’ version ‘1.69.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ainverse.cc -o ainverse.o In file included from ainverse.cc:9: In file included from ./../include/ainverse.h:20: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c eibd.cc -o eibd.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c ggmatmult.f -o ggmatmult.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c gpi.f -o gpi.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c inbreed.cc -o inbreed.o In file included from inbreed.cc:10: In file included from ./../include/inbreed.h:18: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c inverseAdditive.cc -o inverseAdditive.o inverseAdditive.cc:1:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c meuwissen.cc -o meuwissen.o meuwissen.cc:1:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c pedSort.cc -o pedSort.o pedSort.cc:1:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c pedtemplate.cc -o pedtemplate.o In file included from pedtemplate.cc:15: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ pedtemplate.cc:373:21: warning: format specifies type 'int' but the argument has type 'decltype(__x.base() - __y.base())' (aka 'long') [-Wformat] Rprintf("%d\t", p - pedigree.begin()); ~~ ^~~~~~~~~~~~~~~~~~~~ %ld 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c register.cc -o register.o In file included from register.cc:8: In file included from ./../include/meuwissen.h:7: In file included from ./../include/../include/inbreed.h:18: ./../include/pedtemplate.h:18:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sargolzaei.c -o sargolzaei.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sortped.cc -o sortped.o In file included from sortped.cc:1: ./../include/sortped.h:5:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ sortped.cc:55:5: error: use of undeclared identifier 'error' error("Problems in pedigree. Stopping inbreeding calculations\n"); ^ 1 warning and 1 error generated. make: *** [sortped.o] Error 1 ERROR: compilation failed for package ‘GeneticsPed’ * removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/GeneticsPed’