############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rgoslin ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘rgoslin’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ The name of the shared library to be created is: rgoslin.so rm -f "cppgoslin/parser/KnownGrammars.h" rm -f "src/domain/LipidClasses.cpp" rm -f "cppgoslin/domain/ClassesEnum.h" rm -f cppgoslin/domain/*.o rm -f cppgoslin/parser/*.o rm -f cppgoslin/tests/*.o rm -f libcppGoslin.so rm -f *Test rm -f writeGrammarsHeader rm -f writeLipidEnums rm -f libcppGoslin.a clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I . -o writeGrammarsHeader writeGrammarsHeader.cpp && "./writeGrammarsHeader" "cppgoslin/parser/KnownGrammars.h" clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I . -o writeLipidEnums writeLipidEnums.cpp src/domain/StringFunctions.cpp src/parser/SumFormulaParserEventHandler.cpp src/parser/ParserClasses.cpp && "./writeLipidEnums" "src/domain/LipidClasses.cpp" clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/Adduct.o -c src/domain/Adduct.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidMolecularSpecies.o -c src/domain/LipidMolecularSpecies.cpp In file included from src/domain/LipidMolecularSpecies.cpp:26: In file included from ./cppgoslin/domain/LipidMolecularSpecies.h:32: In file included from ./cppgoslin/domain/LipidSpecies.h:36: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidSnPosition.o -c src/domain/LipidSnPosition.cpp In file included from src/domain/LipidSnPosition.cpp:26: In file included from ./cppgoslin/domain/LipidSnPosition.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidStructureDefined.o -c src/domain/LipidStructureDefined.cpp In file included from src/domain/LipidStructureDefined.cpp:26: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/FattyAcid.o -c src/domain/FattyAcid.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidAdduct.o -c src/domain/LipidAdduct.cpp In file included from src/domain/LipidAdduct.cpp:26: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidSpecies.o -c src/domain/LipidSpecies.cpp In file included from src/domain/LipidSpecies.cpp:26: In file included from ./cppgoslin/domain/LipidSpecies.h:36: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidFullStructure.o -c src/domain/LipidFullStructure.cpp In file included from src/domain/LipidFullStructure.cpp:26: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidCompleteStructure.o -c src/domain/LipidCompleteStructure.cpp In file included from src/domain/LipidCompleteStructure.cpp:26: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidSpeciesInfo.o -c src/domain/LipidSpeciesInfo.cpp In file included from src/domain/LipidSpeciesInfo.cpp:26: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/StringFunctions.o -c src/domain/StringFunctions.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/LipidClasses.o -c src/domain/LipidClasses.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/DoubleBonds.o -c src/domain/DoubleBonds.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/FunctionalGroup.o -c src/domain/FunctionalGroup.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/Headgroup.o -c src/domain/Headgroup.cpp In file included from src/domain/Headgroup.cpp:26: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/Cycle.o -c src/domain/Cycle.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/domain/GenericDatastructures.o -c src/domain/GenericDatastructures.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/ParserClasses.o -c src/parser/ParserClasses.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/KnownParsers.o -c src/parser/KnownParsers.cpp In file included from src/parser/KnownParsers.cpp:26: In file included from ./cppgoslin/parser/KnownParsers.h:30: In file included from ./cppgoslin/parser/FattyAcidParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/GoslinParserEventHandler.o -c src/parser/GoslinParserEventHandler.cpp In file included from src/parser/GoslinParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/GoslinParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/LipidMapsParserEventHandler.o -c src/parser/LipidMapsParserEventHandler.cpp In file included from src/parser/LipidMapsParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/LipidMapsParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/SwissLipidsParserEventHandler.o -c src/parser/SwissLipidsParserEventHandler.cpp In file included from src/parser/SwissLipidsParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/SwissLipidsParserEventHandler.h:32: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/HmdbParserEventHandler.o -c src/parser/HmdbParserEventHandler.cpp In file included from src/parser/HmdbParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/HmdbParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/SumFormulaParserEventHandler.o -c src/parser/SumFormulaParserEventHandler.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/SumFormulaParser.o -c src/parser/SumFormulaParser.cpp clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/ShorthandParserEventHandler.o -c src/parser/ShorthandParserEventHandler.cpp In file included from src/parser/ShorthandParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/ShorthandParserEventHandler.h:32: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/FattyAcidParserEventHandler.o -c src/parser/FattyAcidParserEventHandler.cpp In file included from src/parser/FattyAcidParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/FattyAcidParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -falign-functions=64 -Wall -g -O2 -I. -fPIC -o src/parser/LipidBaseParserEventHandler.o -c src/parser/LipidBaseParserEventHandler.cpp In file included from src/parser/LipidBaseParserEventHandler.cpp:26: In file included from ./cppgoslin/parser/LipidBaseParserEventHandler.h:31: In file included from ./cppgoslin/domain/LipidAdduct.h:35: In file included from ./cppgoslin/domain/LipidCompleteStructure.h:31: In file included from ./cppgoslin/domain/LipidFullStructure.h:31: In file included from ./cppgoslin/domain/LipidStructureDefined.h:32: In file included from ./cppgoslin/domain/Headgroup.h:31: ./cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. ar rcs libcppGoslin.a src/domain/Adduct.o src/domain/LipidMolecularSpecies.o src/domain/LipidSnPosition.o src/domain/LipidStructureDefined.o src/domain/FattyAcid.o src/domain/LipidAdduct.o src/domain/LipidSpecies.o src/domain/LipidFullStructure.o src/domain/LipidCompleteStructure.o src/domain/LipidSpeciesInfo.o src/domain/StringFunctions.o src/domain/LipidClasses.o src/domain/DoubleBonds.o src/domain/FunctionalGroup.o src/domain/Headgroup.o src/domain/Cycle.o src/domain/GenericDatastructures.o src/parser/ParserClasses.o src/parser/KnownParsers.o src/parser/GoslinParserEventHandler.o src/parser/LipidMapsParserEventHandler.o src/parser/SwissLipidsParserEventHandler.o src/parser/HmdbParserEventHandler.o src/parser/SumFormulaParserEventHandler.o src/parser/SumFormulaParser.o src/parser/ShorthandParserEventHandler.o src/parser/FattyAcidParserEventHandler.o src/parser/LipidBaseParserEventHandler.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"." -I"./cppgoslin" -I"./cppgoslin/cppgoslin" -I"./cppgoslin/cppgoslin/domain" -I"./cppgoslin/cppgoslin/parser" -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rgoslin.cpp -o rgoslin.o In file included from rgoslin.cpp:3: In file included from ./cppgoslin/cppgoslin/cppgoslin.h:37: In file included from ./cppgoslin/cppgoslin/domain/Headgroup.h:31: ./cppgoslin/cppgoslin/domain/LipidSpeciesInfo.h:53:12: warning: 'LipidSpeciesInfo::to_string' hides overloaded virtual function [-Woverloaded-virtual] string to_string(); ^ ./cppgoslin/cppgoslin/domain/FattyAcid.h:47:12: note: hidden overloaded virtual function 'FattyAcid::to_string' declared here: different number of parameters (1 vs 0) string to_string(LipidLevel level); ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o rgoslin.so RcppExports.o rgoslin.o cppgoslin/libcppGoslin.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-rgoslin/00new/rgoslin/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 (rgoslin)