Failure of xcode build on Apple M1 with macOS Big Sur

[tabe]

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