Bug 3195: Fixed SBML import of function parameters.

Author: shoops

copasi/CMakeLists.txt

@@ -263,7 +263,7 @@ if (APPLE AND CMAKE_GENERATOR STREQUAL "Xcode" OR DISABLE_CORE_OBJECT_LIBRARY)
   endif (ENABLE_OMP)
 else()
   add_library (libCOPASISE-core OBJECT ${COPASI_SOURCES} ${COPASI_HEADERS})
-  # target_compile_options(libCOPASISE-core PRIVATE -Werror -Wall -Wextra -Wsuggest-override)
+  target_compile_options(libCOPASISE-core PRIVATE -fstack-protector-all)
   target_link_libraries(libCOPASISE-core
     ${CROSSGUID_LIBRARY} 
     RAPTOR::RAPTOR

copasi/OpenMP/CRandomContext.cpp

@@ -10,14 +10,23 @@ CRandomContext::CRandomContext(const bool & parallel)
 {}
 
 CRandomContext::~CRandomContext()
-{}
+{
+  if (Base::master())
+    {
+      delete Base::master();
+Base: master() = NULL;
+    }
+}
 
 void  CRandomContext::init(CRandom::Type type, unsigned C_INT32 seed)
 {
   Base::init();
 
   if (Base::master())
-    delete Base::master();
+    {
+      delete Base::master();
+Base: master() = NULL;
+    }
 
   Base::setMaster(nullptr);
 

copasi/model/CReaction.cpp

@@ -717,7 +717,7 @@ CFunction * CReaction::createFunctionFromExpression(const std::string & infix)
         continue;
 
       // Check whether we have compartment with that name
-for (const CCompartment * pCompartment : mChemEq.getCompartments())
+      for (const CCompartment * pCompartment : mChemEq.getCompartments())
         if (pCompartment->getObjectName() == "Name")
           {
             it->setUsage(CFunctionParameter::Role::VOLUME);
@@ -1712,7 +1712,7 @@ CEvaluationNodeVariable* CReaction::object2variable(const CEvaluationNodeObject*
 const CModel * CReaction::getFirstCModelOrDefault(std::map< const CDataObject *, SBase * > & copasi2sbmlmap)
 {
 
-for (auto & pair : copasi2sbmlmap)
+  for (auto & pair : copasi2sbmlmap)
     {
       const CModel * pModel = dynamic_cast<const CModel*>(pair.first->getObjectAncestor("Model"));
 
@@ -1866,16 +1866,15 @@ CFunction * CReaction::setFunctionFromExpressionTree(const CExpression & express
         {
           if (SBMLImporter::areEqualFunctions(pExistingFunction, pTmpFunction))
             {
-
-              setFunction(pExistingFunction);
-
               // The functions and their signature are equal however the role of the variables
               // might not be defined for the existing function if this is the first time it is used
-              mpFunction->setReversible(pTmpFunction->isReversible());
-              mpFunction->getVariables() = pTmpFunction->getVariables();
+              pExistingFunction->setReversible(pTmpFunction->isReversible());
+              pExistingFunction->getVariables() = pTmpFunction->getVariables();
 
               pdelete(pTmpFunction);
 
+              setFunction(pExistingFunction);
+
               // we still need to do the mapping, otherwise global parameters might not be mapped
               it = replacementMap.begin();