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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CancerInSilico
###
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* 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<OffLatticeCell>::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<std::allocator<OffLatticeCell>>::__destroy<OffLatticeCell>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __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<std::allocator<OffLatticeCell>>::destroy<OffLatticeCell>' 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<OffLatticeCell, std::allocator<OffLatticeCell>>::__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<OffLatticeCell, std::allocator<OffLatticeCell>>::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<OffLatticeCell, std::allocator<OffLatticeCell>>::~__vector_base' requested here
vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
^
OffLatticeModel/OffLatticeCellBasedModel.cpp:26:33: note: in instantiation of member function 'std::vector<OffLatticeCell>::vector' requested here
std::vector<OffLatticeCell> 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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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 */ )
^
<inline asm>: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’