libSBML C++ API
5.18.0
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Represents SBML errors and other diagnostics. More...
Classes | |
class | SBMLError |
An error, warning or other diagnostic. More... | |
Represents SBML errors and other diagnostics.
enum SBMLErrorCategory_t |
Category codes for SBMLError diagnostics.
Note that these are distinct from XMLError's category codes. User programs receiving an SBMLError object can use this distinction to check whether the error represents a low-level XML problem or an SBML problem.
Enumerator | |
---|---|
LIBSBML_CAT_SBML |
General SBML error not falling into another category below. |
LIBSBML_CAT_SBML_L1_COMPAT |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model from SBML Level 2 to SBML Level 1. |
LIBSBML_CAT_SBML_L2V1_COMPAT |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 1. |
LIBSBML_CAT_SBML_L2V2_COMPAT |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 2. |
LIBSBML_CAT_GENERAL_CONSISTENCY |
Category of errors that can occur while validating general SBML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
LIBSBML_CAT_IDENTIFIER_CONSISTENCY |
Category of errors that can occur while validating symbol identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
LIBSBML_CAT_UNITS_CONSISTENCY |
Category of errors that can occur while validating the units of measurement on quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
LIBSBML_CAT_MATHML_CONSISTENCY |
Category of errors that can occur while validating MathML formulas in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
LIBSBML_CAT_SBO_CONSISTENCY |
Category of errors that can occur while validating SBO identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
LIBSBML_CAT_OVERDETERMINED_MODEL |
Error in the system of equations in the model: the system is overdetermined, therefore violating a tenet of proper SBML. With respect to the SBML specification, this is validation rule #10601 in the SBML Level 2 Versions 2–4 and Level 3 Versions 1–2 specifications. |
LIBSBML_CAT_SBML_L2V3_COMPAT |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 3. |
LIBSBML_CAT_MODELING_PRACTICE |
Category of warnings about recommended good practices involving SBML and computational modeling. (These are tests performed by libSBML and do not have equivalent SBML validation rules.) |
LIBSBML_CAT_INTERNAL_CONSISTENCY |
Category of errors that can occur while validating libSBML's internal representation of SBML constructs. (These are tests performed by libSBML and do not have equivalent SBML validation rules.) |
LIBSBML_CAT_SBML_L2V4_COMPAT |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 4. |
LIBSBML_CAT_SBML_L3V1_COMPAT |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 3 Version 1. |
LIBSBML_CAT_SBML_L3V2_COMPAT |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 3 Version 1. |
LIBSBML_CAT_SBML_COMPATIBILITY |
Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. |
enum SBMLErrorCode_t |
Codes for all SBML-level errors and warnings from the core specification.
Enumerator | |
---|---|
UnknownError |
Encountered unknown internal libSBML error. |
NotUTF8 |
File does not use UTF-8 encoding. |
UnrecognizedElement |
Encountered unrecognized element. |
NotSchemaConformant |
Document does not conform to the SBML XML schema. |
L3NotSchemaConformant |
Document is not well-formed XML. |
InvalidMathElement |
Invalid MathML. |
DisallowedMathMLSymbol |
Disallowed MathML symbol found. |
DisallowedMathMLEncodingUse |
Use of the MathML 'encoding' attribute is not allowed on this element. |
DisallowedDefinitionURLUse |
Use of the MathML 'definitionURL' attribute is not allowed on this element. |
BadCsymbolDefinitionURLValue |
Invalid |
DisallowedMathTypeAttributeUse |
Use of the MathML 'type' attribute is not allowed on this element. |
DisallowedMathTypeAttributeValue |
Disallowed MathML 'type' attribute value. |
LambdaOnlyAllowedInFunctionDef |
Use of |
BooleanOpsNeedBooleanArgs |
Non-Boolean argument given to Boolean operator. |
NumericOpsNeedNumericArgs |
Non-numerical argument given to numerical operator. |
ArgsToEqNeedSameType |
Arguments to |
PiecewiseNeedsConsistentTypes |
Terms in a |
PieceNeedsBoolean |
The second argument of a |
ApplyCiMustBeUserFunction |
A |
ApplyCiMustBeModelComponent |
A |
KineticLawParametersAreLocalOnly |
Cannot use a KineticLaw local parameter outside of its local scope. |
MathResultMustBeNumeric |
A formula's result in this context must be a numerical value. |
OpsNeedCorrectNumberOfArgs |
Incorrect number of arguments given to MathML operator. |
InvalidNoArgsPassedToFunctionDef |
Incorrect number of arguments given to function invocation. |
DisallowedMathUnitsUse |
Attribute 'units' is only permitted on |
InvalidUnitsValue |
Invalid value given for the 'units' attribute. |
CiCannotReference0DCompartment |
A |
RateOfTargetMustBeCi |
A 'rateOf' |
RateOfTargetCannotBeAssigned |
The target of a 'rateOf' |
RateOfSpeciesTargetCompartmentNot |
Compartments of non-substance |
DuplicateComponentId |
Duplicate 'id' attribute value. |
DuplicateUnitDefinitionId |
Duplicate unit definition 'id' attribute value. |
DuplicateLocalParameterId |
Duplicate local parameter 'id' attribute value. |
MultipleAssignmentOrRateRules |
Multiple rules for the same variable are not allowed. |
MultipleEventAssignmentsForId |
Multiple event assignments for the same variable are not allowed. |
EventAndAssignmentRuleForId |
An event assignment and an assignment rule must not have the same value for 'variable'. |
DuplicateMetaId |
Duplicate 'metaid' attribute value. |
InvalidSBOTermSyntax |
Invalid syntax for an 'sboTerm' attribute value. |
InvalidMetaidSyntax |
Invalid syntax for a 'metaid' attribute value. |
InvalidIdSyntax |
Invalid syntax for an 'id' attribute value. |
InvalidUnitIdSyntax |
Invalid syntax for the identifier of a unit. |
InvalidNameSyntax |
Invalid syntax for a 'name' attribute value. |
DanglingUnitReference |
Dangling reference to a unit. |
MissingAnnotationNamespace |
Missing declaration of the XML namespace for the annotation. |
DuplicateAnnotationNamespaces |
Multiple annotations using the same XML namespace. |
SBMLNamespaceInAnnotation |
The SBML XML namespace cannot be used in an Annotation object. |
MultipleAnnotations |
Only one Annotation object is permitted under a given SBML object. |
InconsistentArgUnits |
The units of the function call's arguments are not consistent with its definition. |
InconsistentKineticLawUnitsL3 |
The kinetic law's units are inconsistent with those of other kinetic laws in the model. |
AssignRuleCompartmentMismatch |
Mismatched units in assignment rule for compartment. |
AssignRuleSpeciesMismatch |
Mismatched units in assignment rule for species. |
AssignRuleParameterMismatch |
Mismatched units in assignment rule for parameter. |
AssignRuleStoichiometryMismatch |
Mismatched units in assignment rule for stoichiometry. |
InitAssignCompartmenMismatch |
Mismatched units in initial assignment to compartment. |
InitAssignSpeciesMismatch |
Mismatched units in initial assignment to species. |
InitAssignParameterMismatch |
Mismatched units in initial assignment to parameter. |
InitAssignStoichiometryMismatch |
Mismatched units in initial assignment to stoichiometry. |
RateRuleCompartmentMismatch |
Mismatched units in rate rule for compartment. |
RateRuleSpeciesMismatch |
Mismatched units in rate rule for species. |
RateRuleParameterMismatch |
Mismatched units in rate rule for parameter. |
RateRuleStoichiometryMismatch |
Mismatched units in rate rule for stoichiometry. |
KineticLawNotSubstancePerTime |
The units of the kinetic law are not 'substance'/'time'. |
SpeciesInvalidExtentUnits |
The species' units are not consistent with units of extent. |
DelayUnitsNotTime |
The units of the delay expression are not units of time. |
EventAssignCompartmentMismatch |
Mismatched units in event assignment for compartment. |
EventAssignSpeciesMismatch |
Mismatched units in event assignment for species. |
EventAssignParameterMismatch |
Mismatched units in event assignment for parameter. |
EventAssignStoichiometryMismatch |
Mismatched units in event assignment for stoichiometry. |
PriorityUnitsNotDimensionless |
The units of a priority expression must be 'dimensionless'. |
UpperUnitBound |
Upper boundary of unit validation diagnostic codes. |
OverdeterminedSystem |
The model is overdetermined. |
InvalidModelSBOTerm |
Invalid 'sboTerm' attribute value for a Model object. |
InvalidFunctionDefSBOTerm |
Invalid 'sboTerm' attribute value for a FunctionDefinition object. |
InvalidParameterSBOTerm |
Invalid 'sboTerm' attribute value for a Parameter object. |
InvalidInitAssignSBOTerm |
Invalid 'sboTerm' attribute value for an InitialAssignment object. |
InvalidRuleSBOTerm |
Invalid 'sboTerm' attribute value for a Rule object. |
InvalidConstraintSBOTerm |
Invalid 'sboTerm' attribute value for a Constraint object. |
InvalidReactionSBOTerm |
Invalid 'sboTerm' attribute value for a Reaction object. |
InvalidSpeciesReferenceSBOTerm |
Invalid 'sboTerm' attribute value for a SpeciesReference object. |
InvalidKineticLawSBOTerm |
Invalid 'sboTerm' attribute value for a KineticLaw object. |
InvalidEventSBOTerm |
Invalid 'sboTerm' attribute value for an Event object. |
InvalidEventAssignmentSBOTerm |
Invalid 'sboTerm' attribute value for an EventAssignment object. |
InvalidCompartmentSBOTerm |
Invalid 'sboTerm' attribute value for a Compartment object. |
InvalidSpeciesSBOTerm |
Invalid 'sboTerm' attribute value for a Species object. |
InvalidCompartmentTypeSBOTerm |
Invalid 'sboTerm' attribute value for a CompartmentType object. |
InvalidSpeciesTypeSBOTerm |
Invalid 'sboTerm' attribute value for a SpeciesType object. |
InvalidTriggerSBOTerm |
Invalid 'sboTerm' attribute value for an Event Trigger object. |
InvalidDelaySBOTerm |
Invalid 'sboTerm' attribute value for an Event Delay object. |
InvalidLocalParameterSBOTerm |
Invalid 'sboTerm' attribute value for a LocalParameter object. |
InvalidSBMLElementSBOTerm |
Invalid 'sboTerm' attribute value for the |
NotesNotInXHTMLNamespace |
Notes must be placed in the XHTML XML namespace. |
NotesContainsXMLDecl |
XML declarations are not permitted in Notes objects. |
NotesContainsDOCTYPE |
XML DOCTYPE elements are not permitted in Notes objects. |
InvalidNotesContent |
Invalid notes content found. |
OnlyOneNotesElementAllowed |
Only one Notes subobject is permitted on a given SBML object. |
InvalidNamespaceOnSBML |
Invalid XML namespace for the SBML container element. |
MissingOrInconsistentLevel |
Missing or inconsistent value for the 'level' attribute. |
MissingOrInconsistentVersion |
Missing or inconsistent value for the 'version' attribute. |
PackageNSMustMatch |
Inconsistent or invalid SBML Level/Version for the package namespace declaration. |
LevelPositiveInteger |
The 'level' attribute must have a positive integer value. |
VersionPositiveInteger |
The 'version' attribute must have a positive integer value. |
AllowedAttributesOnSBML |
Invalid attribute found on the SBML container element. |
L3PackageOnLowerSBML |
An L3 package ns found on the SBML container element. |
MissingModel |
No model definition found. |
IncorrectOrderInModel |
Incorrect ordering of components within the Model object. |
EmptyListElement |
Empty ListOf___ object found. |
NeedCompartmentIfHaveSpecies |
The presence of a species requires a compartment. |
OneOfEachListOf |
Only one of each kind of ListOf___ object is allowed inside a Model object. |
OnlyFuncDefsInListOfFuncDefs |
Only FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions. |
OnlyUnitDefsInListOfUnitDefs |
Only UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects. |
OnlyCompartmentsInListOfCompartments |
Only Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects. |
OnlySpeciesInListOfSpecies |
Only Species, Notes and Annotation objects are allowed in ListOfSpecies objects. |
OnlyParametersInListOfParameters |
Only Parameter, Notes and Annotation objects are allowed in ListOfParameters objects. |
OnlyInitAssignsInListOfInitAssigns |
Only InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects. |
OnlyRulesInListOfRules |
Only Rule, Notes and Annotation objects are allowed in ListOfRules objects. |
OnlyConstraintsInListOfConstraints |
Only Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects. |
OnlyReactionsInListOfReactions |
Only Reaction, Notes and Annotation objects are allowed in ListOfReactions objects. |
OnlyEventsInListOfEvents |
Only Event, Notes and Annotation objects are allowed in ListOfEvents objects. |
L3ConversionFactorOnModel |
A 'conversionFactor' attribute value must reference a Parameter object. |
L3TimeUnitsOnModel |
Invalid 'timeUnits' attribute value. |
L3VolumeUnitsOnModel |
Invalid 'volumeUnits' attribute value. |
L3AreaUnitsOnModel |
Invalid 'areaUnits' attribute value. |
L3LengthUnitsOnModel |
Invalid 'lengthUnits' attribute value. |
L3ExtentUnitsOnModel |
Invalid 'extentUnits' attribute value. |
AllowedAttributesOnModel |
Invalid attribute found on the Model object. |
AllowedAttributesOnListOfFuncs |
Invalid attribute found on the ListOfFunctionDefinitions object. |
AllowedAttributesOnListOfUnitDefs |
Invalid attribute found on the ListOfUnitDefinitions object. |
AllowedAttributesOnListOfComps |
Invalid attribute found on the ListOfCompartments object. |
AllowedAttributesOnListOfSpecies |
Invalid attribute found on the ListOfSpecies object. |
AllowedAttributesOnListOfParams |
Invalid attribute found on the ListOfParameters object. |
AllowedAttributesOnListOfInitAssign |
Invalid attribute found on the ListOfInitialAssignments object. |
AllowedAttributesOnListOfRules |
Invalid attribute found on the ListOfRules object. |
AllowedAttributesOnListOfConstraints |
Invalid attribute found on the ListOfConstraints object. |
AllowedAttributesOnListOfReactions |
Invalid attribute found on the ListOfReactions object. |
AllowedAttributesOnListOfEvents |
Invalid attribute found on the ListOfEvents object. |
L3V2SubstanceUnitsOnModel |
Invalid 'substanceUnits' attribute value. |
FunctionDefMathNotLambda |
Invalid expression found in the function definition. |
InvalidApplyCiInLambda |
Invalid forward reference in the MathML |
RecursiveFunctionDefinition |
Recursive function definitions are not permitted. |
InvalidCiInLambda |
Invalid |
InvalidFunctionDefReturnType |
A function's return type must be either a number or a Boolean. |
OneMathElementPerFunc |
A FunctionDefinition object may contain one |
AllowedAttributesOnFunc |
Invalid attribute found on the FunctionDefinition object. |
OnlyCiInsideBVar | |
InvalidUnitDefId |
Invalid 'id' attribute value for a UnitDefinition object. |
InvalidSubstanceRedefinition |
Invalid redefinition of built-in type 'substance'. |
InvalidLengthRedefinition |
Invalid redefinition of built-in type 'length'. |
InvalidAreaRedefinition |
Invalid redefinition of built-in type name 'area'. |
InvalidTimeRedefinition |
Invalid redefinition of built-in type name 'time'. |
InvalidVolumeRedefinition |
Invalid redefinition of built-in type name 'volume'. |
VolumeLitreDefExponentNotOne |
Must use 'exponent'=1 when defining 'volume' in terms of litres. |
VolumeMetreDefExponentNot3 |
Must use 'exponent'=3 when defining 'volume' in terms of metres. |
EmptyListOfUnits |
An empty list of Unit objects is not permitted in a UnitDefinition object. |
InvalidUnitKind |
Invalid value for the 'kind' attribute of a UnitDefinition object. |
OffsetNoLongerValid |
Unit attribute 'offset' is not supported in this Level+Version of SBML. |
CelsiusNoLongerValid |
Unit name 'Celsius' is not defined in this Level+Version of SBML. |
EmptyUnitListElement |
A ListOfUnits object must not be empty. |
OneListOfUnitsPerUnitDef |
At most one ListOfUnits object is allowed inside a UnitDefinition object. |
OnlyUnitsInListOfUnits |
Only Unit, Notes and Annotation objects are allowed in ListOfUnits objects. |
AllowedAttributesOnUnitDefinition |
Invalid attribute found on the UnitDefinition object. |
AllowedAttributesOnListOfUnits |
Invalid attribute found on the ListOfUnits object. |
AllowedAttributesOnUnit |
Invalid attribute found on the Unit object. |
ZeroDimensionalCompartmentSize |
Invalid use of the 'size' attribute for a zero-dimensional compartment. |
ZeroDimensionalCompartmentUnits |
Invalid use of the 'units' attribute for a zero-dimensional compartment. |
ZeroDimensionalCompartmentConst |
Zero-dimensional compartments must be defined to be constant. |
UndefinedOutsideCompartment |
Invalid value for the 'outside' attribute of a Compartment object. |
RecursiveCompartmentContainment |
Recursive nesting of compartments via the 'outside' attribute is not permitted. |
ZeroDCompartmentContainment |
Invalid nesting of zero-dimensional compartments. |
Invalid1DCompartmentUnits |
Invalid value for the 'units' attribute of a one-dimensional compartment. |
Invalid2DCompartmentUnits |
Invalid value for the 'units' attribute of a two-dimensional compartment. |
Invalid3DCompartmentUnits |
Invalid value for the 'units' attribute of a three-dimensional compartment. |
InvalidCompartmentTypeRef |
Invalid value for the 'compartmentType' attribute of a compartment. |
OneDimensionalCompartmentUnits |
No units defined for 1-D compartment. |
TwoDimensionalCompartmentUnits |
No units defined for 2-D compartment. |
ThreeDimensionalCompartmentUnits |
No units defined for 3-D Compartment object. |
AllowedAttributesOnCompartment |
Invalid attribute found on Compartment object. |
NoUnitsOnCompartment |
No units defined for Compartment object. |
InvalidSpeciesCompartmentRef |
Invalid value found for Species 'compartment' attribute. |
HasOnlySubsNoSpatialUnits |
Attribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true'. |
NoSpatialUnitsInZeroD |
Attribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional. |
NoConcentrationInZeroD |
Attribute 'initialConcentration' must not be set if the compartment is zero-dimensional. |
SpatialUnitsInOneD |
Invalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment. |
SpatialUnitsInTwoD |
Invalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment. |
SpatialUnitsInThreeD |
Invalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment. |
InvalidSpeciesSusbstanceUnits |
Invalid value for a Species 'units' attribute. |
BothAmountAndConcentrationSet |
Cannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously. |
NonBoundarySpeciesAssignedAndUsed |
Cannot use a non-boundary species in both reactions and rules simultaneously. |
NonConstantSpeciesUsed |
Cannot use a constant, non-boundary species as a reactant or product. |
InvalidSpeciesTypeRef |
Invalid value for the 'speciesType' attribute of a species. |
MultSpeciesSameTypeInCompartment |
Cannot have multiple species of the same species type in the same compartment. |
MissingSpeciesCompartment |
Missing value for the 'compartment' attribute. |
SpatialSizeUnitsRemoved |
Attribute 'spatialSizeUnits' is not supported in this Level+Version of SBML. |
SubstanceUnitsOnSpecies |
No substance units defined for the species. |
ConversionFactorOnSpecies |
Invalid value for the 'conversionFactor' attribute. |
AllowedAttributesOnSpecies |
Invalid attribute found on Species object. |
InvalidParameterUnits |
Invalid value for the 'units' attribute of a Parameter object. |
ParameterUnits |
No units defined for the parameter. |
ConversionFactorMustConstant |
A conversion factor must reference a Parameter object declared to be a constant. |
AllowedAttributesOnParameter |
Invalid attribute found on Parameter object. |
InvalidInitAssignSymbol |
Invalid value for the 'symbol' attribute of an InitialAssignment object. |
MultipleInitAssignments |
Multiple initial assignments for the same 'symbol' value are not allowed. |
InitAssignmentAndRuleForSameId |
Cannot set a value using both an initial assignment and an assignment rule simultaneously. |
OneMathElementPerInitialAssign |
An InitialAssignment object may contain one |
AllowedAttributesOnInitialAssign |
Invalid attribute found on an InitialAssignment object. |
InitAssignmentCannotRef0DComp |
InitialAssignment cannot reference 0D compartment. |
InvalidAssignRuleVariable |
Invalid value for the 'variable' attribute of an AssignmentRule object. |
InvalidRateRuleVariable |
Invalid value for the 'variable' attribute of a RateRule object. |
AssignmentToConstantEntity |
An assignment rule cannot assign an entity declared to be constant. |
RateRuleForConstantEntity |
A rate rule cannot assign an entity declared to be constant. |
RepeatedRule10304 | |
CircularRuleDependency |
Circular dependencies involving rules and reactions are not permitted. |
OneMathElementPerRule |
A rule object may contain one |
AllowedAttributesOnAssignRule |
Invalid attribute found on an AssignmentRule object. |
AllowedAttributesOnRateRule |
Invalid attribute found on a RateRule object. |
AllowedAttributesOnAlgRule |
Invalid attribute found on an AlgebraicRule object. |
RuleCannotRef0DComp |
Rule cannot reference 0D compartment. |
CircularDependencyRateOf |
Circular dependencies are not permitted in RateRule and KineticLaw objects. |
ConstraintMathNotBoolean |
A Constraint object's |
IncorrectOrderInConstraint |
Subobjects inside the Constraint object are not in the prescribed order. |
ConstraintNotInXHTMLNamespace |
A Constraint's Message subobject must be in the XHTML XML namespace. |
ConstraintContainsXMLDecl |
XML declarations are not permitted within Constraint's Message objects. |
ConstraintContainsDOCTYPE |
XML DOCTYPE elements are not permitted within Constraint's Message objects. |
InvalidConstraintContent |
Invalid content for a Constraint object's Message object. |
OneMathElementPerConstraint |
A Constraint object may contain one |
OneMessageElementPerConstraint |
A Constraint object can only have one Message subobject. |
AllowedAttributesOnConstraint |
Invalid attribute found on Constraint object. |
NoReactantsOrProducts |
Cannot have a reaction with neither reactants nor products. |
IncorrectOrderInReaction |
Subobjects inside the Reaction object are not in the prescribed order. |
EmptyListInReaction |
Reaction components, if present, cannot be empty. |
InvalidReactantsProductsList |
Invalid object found in the list of reactants or products. |
InvalidModifiersList |
Invalid object found in the list of modifiers. |
OneSubElementPerReaction |
A Reaction object can only contain one of each allowed type of object. |
CompartmentOnReaction |
Invalid value for the Reaction 'compartment' attribute. |
AllowedAttributesOnReaction |
Invalid attribute for a Reaction object. |
InvalidSpeciesReference |
Invalid 'species' attribute value in SpeciesReference object. |
RepeatedRule20611 | |
BothStoichiometryAndMath |
The 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive. |
AllowedAttributesOnSpeciesReference |
Invalid attribute found on the SpeciesReference object. |
AllowedAttributesOnModifier |
Invalid attribute found on the ModifierSpeciesReference object. |
UndeclaredSpeciesRef |
Unknown species referenced in the kinetic law |
IncorrectOrderInKineticLaw |
Incorrect ordering of components in the KineticLaw object. |
EmptyListInKineticLaw |
The list of parameters, if present, cannot be empty. |
NonConstantLocalParameter |
Parameters local to a KineticLaw object must have a 'constant' attribute value of 'true'. |
SubsUnitsNoLongerValid |
Attribute 'substanceUnits' is not supported in this Level+Version of SBML. |
TimeUnitsNoLongerValid |
Attribute 'timeUnits' is not supported in this Level+Version of SBML. |
OneListOfPerKineticLaw |
Only one ListOfLocalParameters object is permitted within a KineticLaw object. |
OnlyLocalParamsInListOfLocalParams |
Only LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects. |
AllowedAttributesOnListOfLocalParam |
Invalid attribute found on the ListOfLocalParameters object. |
OneMathPerKineticLaw |
Only one |
UndeclaredSpeciesInStoichMath |
Unknown species referenced in the StoichiometryMath object's |
AllowedAttributesOnKineticLaw |
Invalid attribute found on the KineticLaw object. |
AllowedAttributesOnListOfSpeciesRef |
Invalid attribute found on the ListOfSpeciesReferences object. |
AllowedAttributesOnListOfMods |
Invalid attribute found on the ListOfModifiers object. |
L3V2FastDeprecated |
Fast attribute deprecated. |
AllowedAttributesOnLocalParameter |
Invalid attribute found on the LocalParameter object. |
LocalParameterShadowsSpecies |
Invalid attribute found on the LocalParameter object. |
MissingTriggerInEvent | |
TriggerMathNotBoolean |
A Trigger object's |
MissingEventAssignment |
The Event object is missing an EventAssignment subobject. |
TimeUnitsEvent |
Units referenced by 'timeUnits' attribute are not compatible with units of time. |
IncorrectOrderInEvent |
Incorrect ordering of components in Event object. |
ValuesFromTriggerTimeNeedDelay |
Attribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay. |
DelayNeedsValuesFromTriggerTime |
The use of a Delay object requires the Event attribute 'useValuesFromTriggerTime'. |
OneMathPerTrigger |
A Trigger object may have one |
OneMathPerDelay |
A Delay object may have one |
InvalidEventAssignmentVariable |
Invalid 'variable' attribute value in Event object. |
EventAssignmentForConstantEntity |
An EventAssignment object cannot assign to a component having attribute 'constant'='true'. |
OneMathPerEventAssignment |
An EventAssignment object may have one |
AllowedAttributesOnEventAssignment |
Invalid attribute found on the EventAssignment object. |
OnlyOneDelayPerEvent | |
OneListOfEventAssignmentsPerEvent |
An Event object can only have one ListOfEventAssignments subobject. |
OnlyEventAssignInListOfEventAssign |
Only EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments. |
AllowedAttributesOnListOfEventAssign |
Invalid attribute found on the ListOfEventAssignments object. |
AllowedAttributesOnEvent |
Invalid attribute found on the Event object. |
AllowedAttributesOnTrigger |
Invalid attribute found on the Trigger object. |
AllowedAttributesOnDelay |
Invalid attribute found on the Delay object. |
PersistentNotBoolean |
The Trigger attribute 'persistent' must evaluate to a Boolean value. |
InitialValueNotBoolean |
The Trigger attribute 'initialValue' must evaluate to a Boolean value. |
OnlyOnePriorityPerEvent | |
OneMathPerPriority |
A Priority object may have one |
AllowedAttributesOnPriority |
Invalid attribute found on the Priority object. |
GeneralWarningNotSpecified |
Unknown error. |
CompartmentShouldHaveSize |
It's best to define a size for every compartment in a model. |
SpeciesShouldHaveValue |
It's best to define an initial amount or initial concentration for every species in a model. |
ParameterShouldHaveUnits |
It's best to declare units for every parameter in a model. |
ParameterShouldHaveValue |
It's best to declare values for every parameter in a model. |
LocalParameterShadowsId |
Local parameters defined within a kinetic law shadow global object symbols. |
LibSBMLAdditionalCodesLowerBound |
Lower boundary of libSBML-specific diagnostic codes. |
CannotConvertToL1V1 |
Cannot convert to SBML Level 1 Version 1. |
NoEventsInL1 |
SBML Level 1 does not support events. |
NoFunctionDefinitionsInL1 |
SBML Level 1 does not support function definitions. |
NoConstraintsInL1 |
SBML Level 1 does not support constraints. |
NoInitialAssignmentsInL1 |
SBML Level 1 does not support initial assignments. |
NoSpeciesTypesInL1 |
SBML Level 1 does not support species types. |
NoCompartmentTypeInL1 |
SBML Level 1 does not support compartment types. |
NoNon3DCompartmentsInL1 |
SBML Level 1 only supports three-dimensional compartments. |
NoFancyStoichiometryMathInL1 |
SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas. |
NoNonIntegerStoichiometryInL1 |
SBML Level 1 does not support non-integer 'stoichiometry' attribute values. |
NoUnitMultipliersOrOffsetsInL1 |
SBML Level 1 does not support multipliers or offsets in unit definitions. |
SpeciesCompartmentRequiredInL1 |
In SBML Level 1, a value for 'compartment' is mandatory in species definitions. |
NoSpeciesSpatialSizeUnitsInL1 |
SBML Level 1 does not support species 'spatialSizeUnits' settings. |
NoSBOTermsInL1 |
SBML Level 1 does not support the 'sboTerm' attribute. |
StrictUnitsRequiredInL1 |
SBML Level 1 requires strict unit consistency. |
ConversionFactorNotInL1 |
SBML Level 1 does not support the 'conversionFactor' attribute. |
CompartmentNotOnL1Reaction |
SBML Level 1 does not support the 'compartment' attribute on Reaction objects. |
ExtentUnitsNotSubstance |
Units of extent must be compatible with units of substance. |
GlobalUnitsNotDeclared |
Global units must be refer to unit kind or unitDefinition. |
HasOnlySubstanceUnitsNotinL1 |
The concept of hasOnlySubstanceUnits was not available in SBML Level 1. |
AvogadroNotSupported |
Avogadro not supported in Levels 2 and 1. |
NoConstraintsInL2v1 |
SBML Level 2 Version 1 does not support Constraint objects. |
NoInitialAssignmentsInL2v1 |
SBML Level 2 Version 1 does not support InitialAssignment objects. |
NoSpeciesTypeInL2v1 |
SBML Level 2 Version 1 does not support SpeciesType objects. |
NoCompartmentTypeInL2v1 |
SBML Level 2 Version 1 does not support CompartmentType objects. |
NoSBOTermsInL2v1 |
SBML Level 2 Version 1 does not support the 'sboTerm' attribute. |
NoIdOnSpeciesReferenceInL2v1 |
SBML Level 2 Version 1 does not support the 'id' attribute on SpeciesReference objects. |
NoDelayedEventAssignmentInL2v1 |
SBML Level 2 Version 1 does not support the 'useValuesFromTriggerTime' attribute. |
StrictUnitsRequiredInL2v1 |
SBML Level 2 Version 1 requires strict unit consistency. |
IntegerSpatialDimensions |
SBML Level 2 Version 1 requires that compartments have spatial dimensions of 0-3. |
StoichiometryMathNotYetSupported |
Conversion to StoichiometryMath objects not yet supported. |
PriorityLostFromL3 |
SBML Level 2 Version 1 does not support priorities on Event objects. |
NonPersistentNotSupported |
SBML Level 2 Version 1 does not support the 'persistent' attribute on Trigger objects. |
InitialValueFalseEventNotSupported |
SBML Level 2 Version 1 does not support the 'initialValue' attribute on Trigger objects. |
SBOTermNotUniversalInL2v2 |
The 'sboTerm' attribute is invalid for this component in SBML Level 2 Version 2. |
NoUnitOffsetInL2v2 |
This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
NoKineticLawTimeUnitsInL2v2 |
This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
NoKineticLawSubstanceUnitsInL2v2 |
This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
NoDelayedEventAssignmentInL2v2 |
This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute. |
ModelSBOBranchChangedBeyondL2v2 |
The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
StrictUnitsRequiredInL2v2 |
SBML Level 2 Version 2 requires strict unit consistency. |
StrictSBORequiredInL2v2 |
SBML Level 2 Version 2 requires strict SBO term consistency. |
DuplicateAnnotationInvalidInL2v2 |
Duplicate top-level annotations are invalid in SBML Level 2 Version 2. |
NoUnitOffsetInL2v3 |
This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
NoKineticLawTimeUnitsInL2v3 |
This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
NoKineticLawSubstanceUnitsInL2v3 |
This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
NoSpeciesSpatialSizeUnitsInL2v3 |
This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects. |
NoEventTimeUnitsInL2v3 |
This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
NoDelayedEventAssignmentInL2v3 |
This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute. |
ModelSBOBranchChangedBeyondL2v3 |
The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
StrictUnitsRequiredInL2v3 |
SBML Level 2 Version 3 requires strict unit consistency. |
StrictSBORequiredInL2v3 |
SBML Level 2 Version 3 requires strict SBO term consistency. |
DuplicateAnnotationInvalidInL2v3 |
Duplicate top-level annotations are invalid in SBML Level 2 Version 3. |
NoUnitOffsetInL2v4 |
This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
NoKineticLawTimeUnitsInL2v4 |
This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
NoKineticLawSubstanceUnitsInL2v4 |
This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
NoSpeciesSpatialSizeUnitsInL2v4 |
This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects. |
NoEventTimeUnitsInL2v4 |
This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
ModelSBOBranchChangedInL2v4 |
The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
DuplicateAnnotationInvalidInL2v4 |
Duplicate top-level annotations are invalid in SBML Level 2 Version 4. |
NoSpeciesTypeInL3v1 |
SBML Level 3 Version 1 does not support SpeciesType objects. |
NoCompartmentTypeInL3v1 |
SBML Level 3 Version 1 does not support CompartmentType objects. |
NoUnitOffsetInL3v1 |
This Level+Version of SBML does not support the 'offset' attribute on Unit objects. |
NoKineticLawTimeUnitsInL3v1 |
This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects. |
NoKineticLawSubstanceUnitsInL3v1 |
This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects. |
NoSpeciesSpatialSizeUnitsInL3v1 |
This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects. |
NoEventTimeUnitsInL3v1 |
This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
ModelSBOBranchChangedInL3v1 |
The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version. |
DuplicateAnnotationInvalidInL3v1 |
Duplicate top-level annotations are invalid in SBML Level 3 Version 1. |
NoCompartmentOutsideInL3v1 |
This Level+Version of SBML does not support the 'outside' attribute on Compartment objects. |
NoStoichiometryMathInL3v1 |
This Level+Version of SBML does not support the StoichiometryMath object. |
DoubleExponentNotSupported |
Exponent of type double not supported in Levels 2 and 1. |
MathMLElementNotSupported |
This MathML element is only permitted in L3V2. |
EmptyListOfElementNotSupported |
Empty 'ListOf' element is only permitted in L3V2. |
MissingMathElementNotSupported |
Missing |
MissingTriggerElementNotSupported |
missing |
BooleanNumericDiscrepancy |
Interchange of Boolean and numeric values only permitted in L3V2. |
IdNameSBaseInL3V2 |
Conversion will lose attributes only available in L3V2 and higher. |
MissingParticipantsNotSupported |
Omission of both |
ConvertibleMathInitialAssignment |
Some L3V2-specific MathML elements are not permitted in InitialAssignment objects. |
FastReactionsNotSupported |
Conversion of reactions employing the 'fast' attribute is not supported. |
SpeciesRefIdInMathMLNotSupported |
This MathML element is only permitted in L3V2. |
InvalidSBMLLevelVersion |
Unknown Level+Version combination of SBML. |
InvalidPackageLevelVersion |
Invalid package Level+Version combination of SBML. |
AnnotationNotesNotAllowedLevel1 |
Annotation objects on the SBML container element are not permitted in SBML Level 1. |
InvalidRuleOrdering |
Invalid ordering of rules. |
RequiredPackagePresent |
The SBML document requires an SBML Level 3 package unavailable in this software. |
UnrequiredPackagePresent |
The SBML document uses an SBML Level 3 package unavailable in this software. |
PackageRequiredShouldBeFalse |
This package expects required to be false. |
SubsUnitsAllowedInKL |
Disallowed value for attribute 'substanceUnits' on KineticLaw object. |
TimeUnitsAllowedInKL |
Disallowed value for attribute 'timeUnits' on KineticLaw object. |
FormulaInLevel1KL |
Only predefined functions are allowed in SBML Level 1 formulas. |
L3SubstanceUnitsOnModel |
Invalid 'substanceUnits' attribute value. |
StoichiometryMathMissingMath |
The |
TimeUnitsRemoved |
This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects. |
BadMathML |
Invalid MathML expression. |
FailedMathMLReadOfDouble |
Missing or invalid floating-point number in MathML expression. |
FailedMathMLReadOfInteger |
Missing or invalid integer in MathML expression. |
FailedMathMLReadOfExponential |
Missing or invalid exponential expression in MathML. |
FailedMathMLReadOfRational |
Missing or invalid rational expression in MathML. |
BadMathMLNodeType |
Invalid MathML element. |
InvalidMathMLAttribute |
Invalid MathML attribute. |
NoTimeSymbolInFunctionDef |
Use of |
NoBodyInFunctionDef |
There must be a |
DanglingUnitSIdRef |
Units must refer to valid unit or unitDefinition. |
RDFMissingAboutTag |
RDF missing the |
RDFEmptyAboutTag |
RDF empty |
RDFAboutTagNotMetaid |
RDF |
RDFNotCompleteModelHistory |
RDF does not contain valid ModelHistory. |
RDFNotModelHistory |
RDF does not result in a ModelHistory. |
AnnotationNotElement |
Annotation must contain element. |
NestedAnnotationNotAllowed |
Nested annotations not allowed. |
InconsistentArgUnitsWarnings |
This is an internal error that reverts to 10501. |
InconsistentPowerUnitsWarnings |
This is an internal error that reverts to 10501. |
InconsistentExponUnitsWarnings |
This is an internal error that reverts to 10501. |
UndeclaredUnits |
Missing unit declarations on parameters or literal numbers in expression. |
UndeclaredTimeUnitsL3 |
Unable to verify consistency of units: the unit of time has not been declared. |
UndeclaredExtentUnitsL3 |
Unable to verify consistency of units: the units of reaction extent have not been declared. |
UndeclaredObjectUnitsL3 |
Unable to verify consistency of units: encountered a model entity with no declared units. |
CannotVerifyUnitsObjectNoMath |
Unable to verify consistency of units: encountered an object with no |
UnrecognisedSBOTerm |
Unrecognized 'sboTerm' attribute value. |
ObseleteSBOTerm |
Obsolete 'sboTerm' attribute value. |
IncorrectCompartmentSpatialDimensions |
In SBML Level 1, only three-dimensional compartments are allowed. |
CompartmentTypeNotValidAttribute |
CompartmentType objects are not available in this Level+Version of SBML. |
ConstantNotValidAttribute |
This Level+Version of SBML does not support the 'constant' attribute on this component. |
MetaIdNotValidAttribute |
Attribute 'metaid' is not available in SBML Level 1. |
SBOTermNotValidAttributeBeforeL2V3 |
The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3. |
InvalidL1CompartmentUnits |
Invalid units for a compartment in SBML Level 1. |
L1V1CompartmentVolumeReqd |
In SBML Level 1, a compartment's volume must be specified. |
CompartmentTypeNotValidComponent |
CompartmentType objects are not available in this Level+Version of SBML. |
ConstraintNotValidComponent |
Constraint objects are not available in this Level+Version of SBML. |
EventNotValidComponent |
Event objects are not available in this Level+Version of SBML. |
SBOTermNotValidAttributeBeforeL2V2 |
The 'sboTerm' attribute is invalid for this component before Level 2 Version 2. |
FuncDefNotValidComponent |
FunctionDefinition objects are not available in this Level+Version of SBML. |
InitialAssignNotValidComponent |
InitialAssignment objects are not available in this Level+Version of SBML. |
VariableNotValidAttribute |
Attribute 'variable' is not available on this component in this Level+Version of SBML. |
UnitsNotValidAttribute |
Attribute 'units' is not available on this component in this Level+Version of SBML. |
ConstantSpeciesNotValidAttribute |
Attribute 'constant' is not available on Species objects in SBML Level 1. |
SpatialSizeUnitsNotValidAttribute |
Attribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1. |
SpeciesTypeNotValidAttribute |
Attribute 'speciesType' is not available on Species objects in SBML Level 1. |
HasOnlySubsUnitsNotValidAttribute |
Attribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1. |
IdNotValidAttribute |
Attribute 'id' is not available on SpeciesReference objects in SBML Level 1. |
NameNotValidAttribute |
Attribute 'name' is not available on SpeciesReference objects in SBML Level 1. |
SpeciesTypeNotValidComponent |
The SpeciesType object is not supported in SBML Level 1. |
StoichiometryMathNotValidComponent |
The StoichiometryMath object is not supported in SBML Level 1. |
MultiplierNotValidAttribute |
Attribute 'multiplier' on Unit objects is not supported in SBML Level 1. |
OffsetNotValidAttribute |
Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1. |
L3SpatialDimensionsUnset |
No value given for 'spatialDimensions' attribute; assuming a value of 3. |
OperationInterrupted |
Operation was interrupted by the user. |
UnknownCoreAttribute |
Encountered an unknown attribute in the SBML Core namespace. |
UnknownPackageAttribute |
Encountered an unknown attribute in an SBML Level 3 package namespace. |
PackageConversionNotSupported |
Conversion of SBML Level 3 package constructs is not yet supported. |
InvalidTargetLevelVersion |
The requested SBML Level/Version combination is not known to exist. |
L3NotSupported |
SBML Level 3 is not yet supported. |
SBMLCodesUpperBound |
Upper boundary of libSBML-specific diagnostic codes. |
enum SBMLErrorSeverity_t |
Severity codes for SBMLError diagnostics.
The only publicly-reported values of this type are the four from XMLErrorSeverity_t. All other values are used internally only, with translation of those codes done in SBMLError.cpp