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flintproject / Flint

A simulator for biological and physiological models
https://flintsimulator.org
MIT License
6 stars 3 forks source link

Failure of xcode build on Apple M1 with macOS Big Sur #26

Open tabe opened 3 years ago

tabe commented 3 years ago

It occurred at linking SOSlib to libSBML.

Environment: macOS 11.4; MacBook Pro (13-inch, M1, 2020) Xcode 12.5.1

mv -f .deps/sensSolver.Tpo .deps/sensSolver.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT solverError.lo -MD -MP -MF .deps/solverError.Tpo -c -o solverError.lo solverError.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT solverError.lo -MD -MP -MF .deps/solverError.Tpo -c solverError.c -fno-common -DPIC -o .libs/solverError.o mv -f .deps/solverError.Tpo .deps/solverError.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT util.lo -MD -MP -MF .deps/util.Tpo -c -o util.lo util.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT util.lo -MD -MP -MF .deps/util.Tpo -c util.c -fno-common -DPIC -o .libs/util.o mv -f .deps/util.Tpo .deps/util.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT data.lo -MD -MP -MF .deps/data.Tpo -c -o data.lo test -f 'private/data.c' || echo './'private/data.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT data.lo -MD -MP -MF .deps/data.Tpo -c private/data.c -fno-common -DPIC -o .libs/data.o mv -f .deps/data.Tpo .deps/data.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT error.lo -MD -MP -MF .deps/error.Tpo -c -o error.lo test -f 'private/error.c' || echo './'private/error.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I/Users/abe/src/Flint/xcode/usr/include -I/Users/abe/src/Flint/xcode/usr/include -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -MT error.lo -MD -MP -MF .deps/error.Tpo -c private/error.c -fno-common -DPIC -o .libs/error.o mv -f .deps/error.Tpo .deps/error.Plo /bin/sh ../libtool --tag=CC --mode=link clang -Wno-unknown-pragmas -Wall -Wextra -ansi -std=iso9899:1990 -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -no-undefined -L/Users/abe/src/Flint/xcode/usr/lib -L/usr/lib -L/Users/abe/src/Flint/xcode/usr/lib -arch x86_64 -mmacosx-version-min=10.11 -headerpad_max_install_names -o libODES.la -rpath /Users/abe/src/Flint/xcode/usr/lib ASTIndexNameNode.lo arithmeticCompiler.lo charBuffer.lo compiler.lo cvodeData.lo cvodeSolver.lo daeSolver.lo drawGraph.lo evaluateAST.lo integratorInstance.lo integratorSettings.lo interpol.lo modelSimplify.lo nullSolver.lo odeConstruct.lo odeModel.lo odeSolver.lo processAST.lo sbml.lo sbmlResults.lo sensSolver.lo solverError.lo util.lo data.lo error.lo -lsbml -lxml2 -lsundials_ida -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial -lm -lm libtool: link: clang -dynamiclib -o .libs/libODES.0.dylib .libs/ASTIndexNameNode.o .libs/arithmeticCompiler.o .libs/charBuffer.o .libs/compiler.o .libs/cvodeData.o .libs/cvodeSolver.o .libs/daeSolver.o .libs/drawGraph.o .libs/evaluateAST.o .libs/integratorInstance.o .libs/integratorSettings.o .libs/interpol.o .libs/modelSimplify.o .libs/nullSolver.o .libs/odeConstruct.o .libs/odeModel.o .libs/odeSolver.o .libs/processAST.o .libs/sbml.o .libs/sbmlResults.o .libs/sensSolver.o .libs/solverError.o .libs/util.o .libs/data.o .libs/error.o -L/Users/abe/src/Flint/xcode/usr/lib -L/usr/lib /Users/abe/src/Flint/xcode/usr/lib/libsbml.dylib -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib -lz -lpthread -licucore -lc++ -lxml2 -lsundials_ida -lsundials_kinsol -lsundials_cvodes -lsundials_nvecserial -lm -arch x86_64 -mmacosx-version-min=10.11 -O2 -g -arch x86_64 -mmacosx-version-min=10.11 -install_name /Users/abe/src/Flint/xcode/usr/lib/libODES.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module Undefined symbols for architecture x86_64: "_ASTNode_addChild", referenced from: _AST_replaceNameByFormula in modelSimplify.o _Species_odeFromReactions in odeConstruct.o _differentiateAST in processAST.o _simplifyAST in processAST.o _determinantNAST in processAST.o _indexAST in processAST.o _copyRevertDataAST in sensSolver.o ... "_ASTNode_create", referenced from: _Species_odeFromReactions in odeConstruct.o _differentiateAST in processAST.o _simplifyAST in processAST.o _determinantNAST in processAST.o _indexAST in processAST.o _copyRevertDataAST in sensSolver.o (maybe you meant: _ASTNode_createIndexName) "_ASTNode_createWithType", referenced from: _ASTNode_createIndexName in ASTIndexNameNode.o _Species_odeFromReactions in odeConstruct.o "_ASTNode_deepCopy", referenced from: _copyAST in processAST.o _differentiateAST in processAST.o _simplifyAST in processAST.o _determinantNAST in processAST.o "_ASTNode_free", referenced from: _AST_replaceFunctionDefinition in modelSimplify.o _Model_reduceToOdes in odeConstruct.o _Species_odeFromReactions in odeConstruct.o _ODEModel_freeDiscontinuities in odeModel.o _ODEModel_free in odeModel.o _ODEModel_freeJacobian in odeModel.o _ODEModel_constructJacobian in odeModel.o ... "_ASTNode_getChild", referenced from: _evaluateAST in evaluateAST.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _Species_odeFromReactions in odeConstruct.o _differentiateAST in processAST.o _simplifyAST in processAST.o _determinantNAST in processAST.o ... "_ASTNode_getInteger", referenced from: _evaluateAST in evaluateAST.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _Model_reduceToOdes in odeConstruct.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o _ODEModel_compileCVODEFunctions in odeModel.o ... "_ASTNode_getLeftChild", referenced from: _simplifyAST in processAST.o "_ASTNode_getListOfNodes", referenced from: _AST_replaceNameByName in modelSimplify.o _AST_replaceNameByValue in modelSimplify.o _AST_replaceNameByParameters in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o ... "_ASTNode_getName", referenced from: _evaluateAST in evaluateAST.o _AST_replaceNameByName in modelSimplify.o _AST_replaceNameByValue in modelSimplify.o _AST_replaceNameByParameters in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_constructJacobian in odeModel.o ... "_ASTNode_getNumChildren", referenced from: _evaluateAST in evaluateAST.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _differentiateAST in processAST.o _simplifyAST in processAST.o _indexAST in processAST.o _ASTNode_getIndices in processAST.o ... "_ASTNode_getReal", referenced from: _evaluateAST in evaluateAST.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _Model_reduceToOdes in odeConstruct.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o _ODEModel_compileCVODEFunctions in odeModel.o ... "_ASTNode_getRightChild", referenced from: _AST_replaceFunctionDefinition in modelSimplify.o _simplifyAST in processAST.o "_ASTNode_getType", referenced from: _ASTNode_getIndex in ASTIndexNameNode.o _ASTNode_setIndex in ASTIndexNameNode.o _ASTNode_isIndexName in ASTIndexNameNode.o _ASTNode_isSetIndex in ASTIndexNameNode.o _ASTNode_isSetData in ASTIndexNameNode.o _ASTNode_setData in ASTIndexNameNode.o _evaluateAST in evaluateAST.o ... "_ASTNode_getUserData", referenced from: _ASTNode_getIndex in ASTIndexNameNode.o _ASTNode_setIndex in ASTIndexNameNode.o _ASTNode_isIndexName in ASTIndexNameNode.o _ASTNode_isSetIndex in ASTIndexNameNode.o _ASTNode_isSetData in ASTIndexNameNode.o _ASTNode_setData in ASTIndexNameNode.o "_ASTNode_isFunction", referenced from: _AST_replaceFunctionDefinition in modelSimplify.o _differentiateAST in processAST.o "_ASTNode_isInteger", referenced from: _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o _ODEModel_compileCVODEFunctions in odeModel.o _ODESense_compileCVODESenseFunctions in odeModel.o _simplifyAST in processAST.o ... "_ASTNode_isLogical", referenced from: _differentiateAST in processAST.o "_ASTNode_isName", referenced from: _AST_replaceNameByName in modelSimplify.o _AST_replaceNameByValue in modelSimplify.o _AST_replaceNameByParameters in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o ... "_ASTNode_isOperator", referenced from: _differentiateAST in processAST.o _simplifyAST in processAST.o "_ASTNode_isReal", referenced from: _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o _ODEModel_compileCVODEFunctions in odeModel.o _ODESense_compileCVODESenseFunctions in odeModel.o _simplifyAST in processAST.o ... "_ASTNode_isRelational", referenced from: _differentiateAST in processAST.o "_ASTNode_isUMinus", referenced from: _simplifyAST in processAST.o "_ASTNode_isUnknown", referenced from: _evaluateAST in evaluateAST.o _differentiateAST in processAST.o "_ASTNode_setCharacter", referenced from: _Species_odeFromReactions in odeConstruct.o "_ASTNode_setInteger", referenced from: _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _Species_odeFromReactions in odeConstruct.o _differentiateAST in processAST.o _simplifyAST in processAST.o _indexAST in processAST.o _copyRevertDataAST in sensSolver.o ... "_ASTNode_setName", referenced from: _AST_replaceNameByName in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _Species_odeFromReactions in odeConstruct.o _differentiateAST in processAST.o _simplifyAST in processAST.o _indexAST in processAST.o ... "_ASTNode_setReal", referenced from: _AST_replaceNameByValue in modelSimplify.o _AST_replaceNameByParameters in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _Species_odeFromReactions in odeConstruct.o _differentiateAST in processAST.o _simplifyAST in processAST.o ... "_ASTNode_setType", referenced from: _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _differentiateAST in processAST.o _simplifyAST in processAST.o _determinantNAST in processAST.o _indexAST in processAST.o _copyRevertDataAST in sensSolver.o ... "_ASTNode_setUserData", referenced from: _ASTNode_createIndexName in ASTIndexNameNode.o _ASTNode_setIndex in ASTIndexNameNode.o _ASTNode_setData in ASTIndexNameNode.o "_ASTNode_swapChildren", referenced from: _AST_replaceFunctionDefinition in modelSimplify.o "_List_add", referenced from: _topoSort in odeModel.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o _ASTNode_getIndices in processAST.o _SolverError_error in solverError.o "_List_create", referenced from: _topoSort in odeModel.o _ODEModel_constructJacobian in odeModel.o _ODESense_create in odeModel.o _ASTNode_getIndexArray in processAST.o _SolverError_error in solverError.o "_List_free", referenced from: _AST_replaceNameByName in modelSimplify.o _AST_replaceNameByValue in modelSimplify.o _AST_replaceNameByParameters in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_topologicalRuleSort in odeModel.o _topoSort in odeModel.o ... "_List_get", referenced from: _AST_replaceNameByName in modelSimplify.o _AST_replaceNameByValue in modelSimplify.o _AST_replaceNameByParameters in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_topologicalRuleSort in odeModel.o _ODEModel_constructJacobian in odeModel.o ... "_List_remove", referenced from: _ODEModel_topologicalRuleSort in odeModel.o _topoSort in odeModel.o _ASTNode_getIndexArray in processAST.o _SolverError_clear in solverError.o "_List_size", referenced from: _AST_replaceNameByName in modelSimplify.o _AST_replaceNameByValue in modelSimplify.o _AST_replaceNameByParameters in modelSimplify.o _AST_replaceNameByFormula in modelSimplify.o _AST_replaceFunctionDefinition in modelSimplify.o _ODEModel_topologicalRuleSort in odeModel.o _topoSort in odeModel.o ... "_SBML_formulaToString", referenced from: _drawModel in drawGraph.o _IntegratorInstance_updateData in integratorInstance.o _IntegratorInstance_checkTrigger in integratorInstance.o _AST_dump in processAST.o _IntegratorInstance_printQuad in sensSolver.o "_SBML_parseFormula", referenced from: _IntegratorInstance_setLinearObjectiveFunction in sensSolver.o _IntegratorInstance_setObjectiveFunction in sensSolver.o _IntegratorInstance_setObjectiveFunctionFromString in sensSolver.o "_XMLError_getErrorId", referenced from: _parseModel in sbml.o _convertModel in sbml.o "_XMLError_getMessage", referenced from: _parseModel in sbml.o _convertModel in sbml.o "_XMLError_getSeverity", referenced from: _parseModel in sbml.o _convertModel in sbml.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: [libODES.la] Error 1 make[2]: [all] Error 2 make[1]: [all-recursive] Error 1 make: [tmp/SBML_odeSolver-1.9.0.installed] Error 2