############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GrafGen ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘GrafGen’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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 -c AncestrySnps.cpp -o AncestrySnps.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 -c BedFileSnpGeno.cpp -o BedFileSnpGeno.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 -c BimFileAncestrySnps.cpp -o BimFileAncestrySnps.o BimFileAncestrySnps.cpp:144:9: warning: variable 'numSwaps' set but not used [-Wunused-but-set-variable] int numSwaps = 0; ^ 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 -c FamFileSamples.cpp -o FamFileSamples.o FamFileSamples.cpp:65:9: warning: variable 'lineNo' set but not used [-Wunused-but-set-variable] int lineNo = 0; ^ 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 GrafGenHp_init.c -o GrafGenHp_init.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 -c GrafPop.cpp -o GrafPop.o In file included from GrafPop.cpp:1: ./GrafPop.h:1:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 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 -c SampleGenoAncestry.cpp -o SampleGenoAncestry.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 -c SampleGenoDist.cpp -o SampleGenoDist.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 -c Util.cpp -o Util.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 -c VcfSampleAncestrySnpGeno.cpp -o VcfSampleAncestrySnpGeno.o VcfSampleAncestrySnpGeno.cpp:93:9: warning: variable 'buffNo' set but not used [-Wunused-but-set-variable] int buffNo = 0; ^ VcfSampleAncestrySnpGeno.cpp:312:9: warning: variable 'ancSnpNo' set but not used [-Wunused-but-set-variable] int ancSnpNo = 0; // Final list of ancestry SNPs to be used for ancestry inference ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GrafGen.so AncestrySnps.o BedFileSnpGeno.o BimFileAncestrySnps.o FamFileSamples.o GrafGenHp_init.o GrafPop.o SampleGenoAncestry.o SampleGenoDist.o Util.o VcfSampleAncestrySnpGeno.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-GrafGen/00new/GrafGen/libs ** R ** data ** 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 (GrafGen)