############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CancerInSilico ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘CancerInSilico’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RunModel.cpp -o RunModel.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OffLatticeModel/OffLatticeCellBasedModel.cpp -o OffLatticeModel/OffLatticeCellBasedModel.o In file included from OffLatticeModel/OffLatticeCellBasedModel.cpp:1: In file included from OffLatticeModel/OffLatticeCellBasedModel.h:6: In file included from OffLatticeModel/../Core/CellBasedModel.h:6: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/unordered_map:411: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__hash_table:15: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:86: warning: destructor called on non-final 'OffLatticeCell' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator::destroy' requested here __a.destroy(__p); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits>::__destroy' requested here {__destroy(__has_destroy(), __a, __p);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits>::destroy' requested here __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base>::__destruct_at_end' requested here void clear() _NOEXCEPT {__destruct_at_end(__begin_);} ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base>::clear' requested here clear(); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:497:5: note: in instantiation of member function 'std::__vector_base>::~__vector_base' requested here vector() _NOEXCEPT_(is_nothrow_default_constructible::value) ^ OffLatticeModel/OffLatticeCellBasedModel.cpp:26:33: note: in instantiation of member function 'std::vector::vector' requested here std::vector defaultCells; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: qualify call to silence this warning _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();} ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Core/Cell.cpp -o Core/Cell.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Core/CellType.cpp -o Core/CellType.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Core/Drug.cpp -o Core/Drug.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Core/Random.cpp -o Core/Random.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Tests/Core/test-CellType.cpp -o Tests/Core/test-CellType.o Tests/Core/test-CellType.cpp:18:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type0.name() == "DEFAULT"); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:19:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type0.id() == 0); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:20:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type0.size() == 1.0); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:21:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type0.minCycle() == 48); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:22:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type0.cycleLength() == 48); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:28:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type1.name() == "DOUBLE_SIZE"); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:29:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type1.id() == 1); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:30:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type1.size() == 2.0); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:31:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type1.minCycle() == 48); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ Tests/Core/test-CellType.cpp:32:9: error: unrecognized instruction mnemonic, did you mean: bit, cnt, hint, ins, not? REQUIRE(type1.cycleLength() == 48); ^ Tests/Core/../catch.h:11513:25: note: expanded from macro 'REQUIRE' #define REQUIRE( expr ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, expr ) ^ Tests/Core/../catch.h:2162:9: note: expanded from macro 'INTERNAL_CATCH_TEST' INTERNAL_CATCH_REACT( __catchResult ) \ ^ Tests/Core/../catch.h:2146:44: note: expanded from macro 'INTERNAL_CATCH_REACT' if( resultBuilder.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ ^ Tests/Core/../catch.h:2082:75: note: expanded from macro 'CATCH_BREAK_INTO_DEBUGGER' #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } ^ Tests/Core/../catch.h:2060:38: note: expanded from macro 'CATCH_TRAP' #define CATCH_TRAP() __asm__("int $3\n" : : /* NOLINT */ ) ^ :1:2: note: instantiated into assembly here int $3 ^ 10 errors generated. make: *** [Tests/Core/test-CellType.o] Error 1 ERROR: compilation failed for package ‘CancerInSilico’ * removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CancerInSilico’