libSBML C API
libSBML 5.8.0 C API
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Representation of errors, warnings and other diagnostics.
This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
When a libSBML operation on SBML content results in an error, or when there is something wrong with the SBML content, the problems are reported as SBMLError objects. These are generally stored in an SBMLErrorLog object; this log object, in turn, is kept in the SBMLDocument object containing the SBML content. Applications can obtain the list of logged errors using SBMLDocument::getErrorLog() and then use the methods provided by SBMLErrorLog to access individual SBMLError objects. (Note that despite the word "error" in the name, SBMLError objects are used to represent not only "true" errors, but also warnings and some informational diagnostics. The name is a historical hold-over from early versions of libSBML, in which the object really was only used to report errors.)
Error codes are useful mainly for software. For human readers, SBMLError also includes text messages that describe the nature of a given problem. The messages can be accessed using SBMLError::getShortMessage() and SBMLError::getMessage(). The former provides a brief one-line description of the issue, while SBMLError::getMessage() provides a more detailed text, including (if appropriate) references to sections of the SBML specifications where relevant topics are discussed. These text strings are suitable for displaying to human users.
In addition, SBMLError also has a severity code. Its value may be retrieved using the method SBMLError::getSeverity(). The possible severity values are the same as those reported by Severity levels currently range from informational (LIBSBML_SEV_INFO) to fatal errors (LIBSBML_SEV_FATAL). They can be used by an application to evaluate how serious a given problem is.
Finally, SBMLError records the line and column near where the problem occurred in the SBML content. The values may be retrieved using the methods SBMLError::getLine() and SBMLError::getColumn(). We say "near", because a lot of factors affect how accurate the line/column information ultimately is. For example, different XML parsers have different conventions for which line and column number they report for a particular problem (which makes a difference when a problem involves an opening XML tag on one line and a closing tag on another line). In some situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the SBMLError object to the the value of the maximum unsigned long integer representable on the platform where libSBML is running. (This is equal to the constant named ULONG_MAX
in C and C++.) The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
N | = Not applicable |
I | = Informational |
W | = Warning |
E | = Error |
F | = Fatal |
The text shown in the "Meaning" is the text returned by the SBMLError::getShortMessage() method on a given SBMLError object. A longer and (hopefully) clearer explanation of the issue is returned by SBMLError::getMessage().
Enumerator | Meaning | L 1 V 1 | L 1 V 2 | L 2 V 1 | L 2 V 2 | L 2 V 3 | L 2 V 4 | L 3 V 1 |
---|---|---|---|---|---|---|---|---|
UnknownError | Encountered unknown internal libSBML error | F | F | F | F | F | F | F |
NotUTF8 | File does not use UTF-8 encoding | E | E | E | E | E | E | E |
UnrecognizedElement | Encountered unrecognized element | E | E | E | E | E | E | E |
NotSchemaConformant | Document does not conform to the SBML XML schema | E | E | E | E | E | E | E |
L3NotSchemaConformant | Document is not well-formed XML | N | N | N | N | N | N | E |
InvalidMathElement | Invalid MathML | N | N | E | E | E | E | E |
DisallowedMathMLSymbol | Disallowed MathML symbol found | N | N | E | E | E | E | E |
DisallowedMathMLEncodingUse | Use of the MathML 'encoding' attribute is not allowed on this element | N | N | E | E | E | E | E |
DisallowedDefinitionURLUse | Use of the MathML 'definitionURL' attribute is not allowed on this element | N | N | E | E | E | E | E |
BadCsymbolDefinitionURLValue | Invalid <csymbol> 'definitionURL' attribute value | N | N | E | E | E | E | E |
DisallowedMathTypeAttributeUse | Use of the MathML 'type' attribute is not allowed on this element | N | N | E | E | E | E | E |
DisallowedMathTypeAttributeValue | Disallowed MathML 'type' attribute value | N | N | E | E | E | E | E |
LambdaOnlyAllowedInFunctionDef | Use of <lambda> not permitted outside of FunctionDefinition objects | N | N | E | E | E | E | E |
BooleanOpsNeedBooleanArgs | Non-Boolean argument given to Boolean operator | N | N | W | E | E | E | E |
NumericOpsNeedNumericArgs | Non-numerical argument given to numerical operator | N | N | W | E | E | E | E |
ArgsToEqNeedSameType | Arguments to <eq> and <neq> must have the same data types | N | N | W | E | E | E | E |
PiecewiseNeedsConsistentTypes | Terms in a <piecewise> expression must have consistent data types | N | N | W | E | E | E | E |
PieceNeedsBoolean | The second argument of a <piece> expression must yield a Boolean value | N | N | W | E | E | E | E |
ApplyCiMustBeUserFunction | A <ci> element in this context must refer to a function definition | N | N | W | E | E | E | E |
ApplyCiMustBeModelComponent | A <ci> element in this context must refer to a model component | N | N | W | E | E | E | E |
KineticLawParametersAreLocalOnly | Cannot use a KineticLaw local parameter outside of its local scope | N | N | W | E | E | E | E |
MathResultMustBeNumeric | A formula's result in this context must be a numerical value | N | N | W | E | E | E | E |
OpsNeedCorrectNumberOfArgs | Incorrect number of arguments given to MathML operator | N | N | W | E | E | E | E |
InvalidNoArgsPassedToFunctionDef | Incorrect number of arguments given to function invocation | N | N | N | N | N | E | E |
DisallowedMathUnitsUse | Attribute 'units' is only permitted on <cn> elements | N | N | N | N | N | N | E |
InvalidUnitsValue | Invalid value given for the 'units' attribute | N | N | N | N | N | N | E |
DuplicateComponentId | Duplicate 'id' attribute value | E | E | E | E | E | E | E |
DuplicateUnitDefinitionId | Duplicate unit definition 'id' attribute value | E | E | E | E | E | E | E |
DuplicateLocalParameterId | Duplicate local parameter 'id' attribute value | E | E | E | E | E | E | E |
MultipleAssignmentOrRateRules | Multiple rules for the same variable are not allowed | E | E | E | E | E | E | E |
MultipleEventAssignmentsForId | Multiple event assignments for the same variable are not allowed | N | N | E | E | E | E | E |
EventAndAssignmentRuleForId | An event assignment and an assignment rule must not have the same value for 'variable' | N | N | E | E | E | E | E |
DuplicateMetaId | Duplicate 'metaid' attribute value | N | N | E | E | E | E | E |
InvalidSBOTermSyntax | Invalid syntax for an 'sboTerm' attribute value | N | N | N | E | E | E | E |
InvalidMetaidSyntax | Invalid syntax for a 'metaid' attribute value | N | N | E | E | E | E | E |
InvalidIdSyntax | Invalid syntax for an 'id' attribute value | E | E | E | E | E | E | E |
InvalidUnitIdSyntax | Invalid syntax for the identifier of a unit | N | N | N | E | E | E | E |
InvalidNameSyntax | Invalid syntax for a 'name' attribute value | N | N | N | N | N | N | E |
MissingAnnotationNamespace | Missing declaration of the XML namespace for the annotation | N | N | N | E | E | E | E |
DuplicateAnnotationNamespaces | Multiple annotations using the same XML namespace | N | N | N | E | E | E | E |
SBMLNamespaceInAnnotation | The SBML XML namespace cannot be used in an Annotation object | N | N | N | E | E | E | N |
MultipleAnnotations | Only one Annotation object is permitted under a given SBML object | N | N | N | N | N | N | E |
InconsistentArgUnits | The units of the function call's arguments are not consistent with its definition | W | W | W | E | E | W | W |
InconsistentKineticLawUnitsL3 | The kinetic law's units are inconsistent with those of other kinetic laws in the model | N | N | N | N | N | N | W |
AssignRuleCompartmentMismatch | Mismatched units in assignment rule for compartment | E | E | E | E | E | W | W |
AssignRuleSpeciesMismatch | Mismatched units in assignment rule for species | E | E | E | E | E | W | W |
AssignRuleParameterMismatch | Mismatched units in assignment rule for parameter | E | E | E | E | E | W | W |
AssignRuleStoichiometryMismatch | Mismatched units in assignment rule for stoichiometry | N | N | N | N | N | N | W |
InitAssignCompartmenMismatch | Mismatched units in initial assignment to compartment | N | N | N | E | E | W | W |
InitAssignSpeciesMismatch | Mismatched units in initial assignment to species | N | N | N | E | E | W | W |
InitAssignParameterMismatch | Mismatched units in initial assignment to parameter | N | N | N | E | E | W | W |
InitAssignStoichiometryMismatch | Mismatched units in initial assignment to stoichiometry | N | N | N | N | N | N | W |
RateRuleCompartmentMismatch | Mismatched units in rate rule for compartment | E | E | E | E | E | W | W |
RateRuleSpeciesMismatch | Mismatched units in rate rule for species | E | E | E | E | E | W | W |
RateRuleParameterMismatch | Mismatched units in rate rule for parameter | E | E | E | E | E | W | W |
RateRuleStoichiometryMismatch | Mismatched units in rate rule for stoichiometry | N | N | N | N | N | N | W |
KineticLawNotSubstancePerTime | The units of the kinetic law are not 'substance'/'time' | E | E | E | E | E | W | W |
SpeciesInvalidExtentUnits | The species' units are not consistent with units of extent | N | N | N | N | N | N | W |
DelayUnitsNotTime | The units of the delay expression are not units of time | N | N | E | E | E | W | W |
EventAssignCompartmentMismatch | Mismatched units in event assignment for compartment | N | N | E | E | E | W | W |
EventAssignSpeciesMismatch | Mismatched units in event assignment for species | N | N | E | E | E | W | W |
EventAssignParameterMismatch | Mismatched units in event assignment for parameter | N | N | E | E | E | W | W |
EventAssignStoichiometryMismatch | Mismatched units in event assignment for stoichiometry | N | N | N | N | N | N | W |
PriorityUnitsNotDimensionless | The units of a priority expression must be 'dimensionless' | N | N | N | N | N | N | W |
UpperUnitBound | Upper boundary of unit validation diagnostic codes | N | N | N | N | N | N | N |
OverdeterminedSystem | The model is overdetermined | W | W | W | E | E | E | E |
InvalidModelSBOTerm | Invalid 'sboTerm' attribute value for a Model object | N | N | N | E | E | W | W |
InvalidFunctionDefSBOTerm | Invalid 'sboTerm' attribute value for a FunctionDefinition object | N | N | N | E | E | W | W |
InvalidParameterSBOTerm | Invalid 'sboTerm' attribute value for a Parameter object | N | N | N | E | E | W | W |
InvalidInitAssignSBOTerm | Invalid 'sboTerm' attribute value for an InitialAssignment object | N | N | N | E | E | W | W |
InvalidRuleSBOTerm | Invalid 'sboTerm' attribute value for a Rule object | N | N | N | E | E | W | W |
InvalidConstraintSBOTerm | Invalid 'sboTerm' attribute value for a Constraint object | N | N | N | E | E | W | W |
InvalidReactionSBOTerm | Invalid 'sboTerm' attribute value for a Reaction object | N | N | N | E | E | W | W |
InvalidSpeciesReferenceSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesReference object | N | N | N | E | E | W | W |
InvalidKineticLawSBOTerm | Invalid 'sboTerm' attribute value for a KineticLaw object | N | N | N | E | E | W | W |
InvalidEventSBOTerm | Invalid 'sboTerm' attribute value for an Event object | N | N | N | E | E | W | W |
InvalidEventAssignmentSBOTerm | Invalid 'sboTerm' attribute value for an EventAssignment object | N | N | N | E | E | W | W |
InvalidCompartmentSBOTerm | Invalid 'sboTerm' attribute value for a Compartment object | N | N | N | N | E | W | W |
InvalidSpeciesSBOTerm | Invalid 'sboTerm' attribute value for a Species object | N | N | N | N | E | W | W |
InvalidCompartmentTypeSBOTerm | Invalid 'sboTerm' attribute value for a CompartmentType object | N | N | N | N | E | W | N |
InvalidSpeciesTypeSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesType object | N | N | N | N | E | W | N |
InvalidTriggerSBOTerm | Invalid 'sboTerm' attribute value for an Event Trigger object | N | N | N | N | E | W | W |
InvalidDelaySBOTerm | Invalid 'sboTerm' attribute value for an Event Delay object | N | N | N | N | E | W | W |
NotesNotInXHTMLNamespace | Notes must be placed in the XHTML XML namespace | E | E | E | E | E | E | E |
NotesContainsXMLDecl | XML declarations are not permitted in Notes objects | N | N | N | E | E | E | E |
NotesContainsDOCTYPE | XML DOCTYPE elements are not permitted in Notes objects | N | N | N | E | E | E | E |
InvalidNotesContent | Invalid notes content found | N | N | N | E | E | E | N |
OnlyOneNotesElementAllowed | Only one Notes subobject is permitted on a given SBML object | N | N | N | N | N | N | E |
InvalidNamespaceOnSBML | Invalid XML namespace for the SBML container element | E | E | E | E | E | E | E |
MissingOrInconsistentLevel | Missing or inconsistent value for the 'level' attribute | E | E | E | E | E | E | E |
MissingOrInconsistentVersion | Missing or inconsistent value for the 'version' attribute | E | E | E | E | E | E | E |
PackageNSMustMatch | Inconsistent or invalid SBML Level/Version for the package namespace declaration | N | N | N | N | N | N | E |
LevelPositiveInteger | The 'level' attribute must have a positive integer value | N | N | N | N | N | N | E |
VersionPositiveInteger | The 'version' attribute must have a positive integer value | N | N | N | N | N | N | E |
AllowedAttributesOnSBML | Invalid attribute found on the SBML container element | N | N | N | N | N | N | E |
L3PackageOnLowerSBML | An L3 package ns found on the SBML container element. | W | W | W | W | W | W | N |
MissingModel | No model definition found | E | E | E | E | E | E | E |
IncorrectOrderInModel | Incorrect ordering of components within the Model object | E | E | E | E | E | E | N |
EmptyListElement | Empty ListOf___ object found | E | E | E | E | E | E | E |
NeedCompartmentIfHaveSpecies | The presence of a species requires a compartment | E | E | E | E | E | E | E |
OneOfEachListOf | Only one of each kind of ListOf___ object is allowed inside a Model object | N | N | N | N | N | N | E |
OnlyFuncDefsInListOfFuncDefs | Only FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions | N | N | N | N | N | N | E |
OnlyUnitDefsInListOfUnitDefs | Only UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects | N | N | N | N | N | N | E |
OnlyCompartmentsInListOfCompartments | Only Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects | N | N | N | N | N | N | E |
OnlySpeciesInListOfSpecies | Only Species, Notes and Annotation objects are allowed in ListOfSpecies objects | N | N | N | N | N | N | E |
OnlyParametersInListOfParameters | Only Parameter, Notes and Annotation objects are allowed in ListOfParameters objects | N | N | N | N | N | N | E |
OnlyInitAssignsInListOfInitAssigns | Only InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects | N | N | N | N | N | N | E |
OnlyRulesInListOfRules | Only Rule, Notes and Annotation objects are allowed in ListOfRules objects | N | N | N | N | N | N | E |
OnlyConstraintsInListOfConstraints | Only Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects | N | N | N | N | N | N | E |
OnlyReactionsInListOfReactions | Only Reaction, Notes and Annotation objects are allowed in ListOfReactions objects | N | N | N | N | N | N | E |
OnlyEventsInListOfEvents | Only Event, Notes and Annotation objects are allowed in ListOfEvents objects | N | N | N | N | N | N | E |
L3ConversionFactorOnModel | A 'conversionFactor' attribute value must reference a Parameter object | N | N | N | N | N | N | E |
L3TimeUnitsOnModel | Invalid 'timeUnits' attribute value | N | N | N | N | N | N | W |
L3VolumeUnitsOnModel | Invalid 'volumeUnits' attribute value | N | N | N | N | N | N | W |
L3AreaUnitsOnModel | Invalid 'areaUnits' attribute value | N | N | N | N | N | N | W |
L3LengthUnitsOnModel | Invalid 'lengthUnits' attribute value | N | N | N | N | N | N | W |
L3ExtentUnitsOnModel | Invalid 'extentUnits' attribute value | N | N | N | N | N | N | W |
AllowedAttributesOnModel | Invalid attribute found on the Model object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfFuncs | Invalid attribute found on the ListOfFunctionDefinitions object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfUnitDefs | Invalid attribute found on the ListOfUnitDefinitions object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfComps | Invalid attribute found on the ListOfCompartments object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfSpecies | Invalid attribute found on the ListOfSpecies object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfParams | Invalid attribute found on the ListOfParameters object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfInitAssign | Invalid attribute found on the ListOfInitialAssignments object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfRules | Invalid attribute found on the ListOfRules object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfConstraints | Invalid attribute found on the ListOfConstraints object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfReactions | Invalid attribute found on the ListOfReactions object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfEvents | Invalid attribute found on the ListOfEvents object | N | N | N | N | N | N | E |
FunctionDefMathNotLambda | Invalid expression found in the function definition | N | N | E | E | E | E | E |
InvalidApplyCiInLambda | Invalid forward reference in the MathML <apply> <ci> ...</ci> </apply> expression | N | N | E | E | E | N | N |
RecursiveFunctionDefinition | Recursive function definitions are not permitted | N | N | E | E | E | E | E |
InvalidCiInLambda | Invalid <ci> reference found inside the <lambda> mathematical formula | N | N | E | E | E | E | E |
InvalidFunctionDefReturnType | A function's return type must be either a number or a Boolean | N | N | E | E | E | E | E |
OneMathElementPerFunc | A FunctionDefinition object must contain one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnFunc | Invalid attribute found on the FunctionDefinition object | N | N | N | N | N | N | E |
InvalidUnitDefId | Invalid 'id' attribute value for a UnitDefinition object | E | E | E | E | E | E | E |
InvalidSubstanceRedefinition | Invalid redefinition of built-in type 'substance' | E | E | E | E | E | E | N |
InvalidLengthRedefinition | Invalid redefinition of built-in type 'length' | W | W | E | E | E | E | N |
InvalidAreaRedefinition | Invalid redefinition of built-in type name 'area' | W | W | E | E | E | E | N |
InvalidTimeRedefinition | Invalid redefinition of built-in type name 'time' | E | E | E | E | E | E | N |
InvalidVolumeRedefinition | Invalid redefinition of built-in type name 'volume' | E | E | E | E | E | E | N |
VolumeLitreDefExponentNotOne | Must use 'exponent'=1 when defining 'volume' in terms of litres | E | E | E | E | E | N | N |
VolumeMetreDefExponentNot3 | Must use 'exponent'=3 when defining 'volume' in terms of metres | N | N | E | E | E | N | N |
EmptyListOfUnits | An empty list of Unit objects is not permitted in a UnitDefinition object | E | E | E | E | E | E | N |
InvalidUnitKind | Invalid value for the 'kind' attribute of a UnitDefinition object | E | E | E | E | E | E | E |
OffsetNoLongerValid | Unit attribute 'offset' is not supported in this Level+Version of SBML | N | N | N | E | E | E | N |
CelsiusNoLongerValid | Unit name 'Celsius' is not defined in this Level+Version of SBML | N | N | N | E | E | E | N |
EmptyUnitListElement | A ListOfUnits object must not be empty | N | N | N | N | N | N | E |
OneListOfUnitsPerUnitDef | At most one ListOfUnits object is allowed inside a UnitDefinition object | N | N | N | N | N | N | E |
OnlyUnitsInListOfUnits | Only Unit, Notes and Annotation objects are allowed in ListOfUnits objects | N | N | N | N | N | N | E |
AllowedAttributesOnUnitDefinition | Invalid attribute found on the UnitDefinition object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfUnits | Invalid attribute found on the ListOfUnits object | N | N | N | N | N | N | E |
AllowedAttributesOnUnit | Invalid attribute found on the Unit object | N | N | N | N | N | N | E |
ZeroDimensionalCompartmentSize | Invalid use of the 'size' attribute for a zero-dimensional compartment | N | N | E | E | E | E | N |
ZeroDimensionalCompartmentUnits | Invalid use of the 'units' attribute for a zero-dimensional compartment | N | N | E | E | E | E | N |
ZeroDimensionalCompartmentConst | Zero-dimensional compartments must be defined to be constant | N | N | E | E | E | E | N |
UndefinedOutsideCompartment | Invalid value for the 'outside' attribute of a Compartment object | E | E | E | E | E | E | N |
RecursiveCompartmentContainment | Recursive nesting of compartments via the 'outside' attribute is not permitted | W | W | W | E | E | E | N |
ZeroDCompartmentContainment | Invalid nesting of zero-dimensional compartments | N | N | W | E | E | E | N |
Invalid1DCompartmentUnits | Invalid value for the 'units' attribute of a one-dimensional compartment | N | N | E | E | E | E | W |
Invalid2DCompartmentUnits | Invalid value for the 'units' attribute of a two-dimensional compartment | N | N | E | E | E | E | W |
Invalid3DCompartmentUnits | Invalid value for the 'units' attribute of a three-dimensional compartment | E | E | E | E | E | E | W |
InvalidCompartmentTypeRef | Invalid value for the 'compartmentType' attribute of a compartment | N | N | N | E | E | E | N |
OneDimensionalCompartmentUnits | No units defined for 1-D compartment | N | N | N | N | N | N | W |
TwoDimensionalCompartmentUnits | No units defined for 2-D compartment | N | N | N | N | N | N | W |
ThreeDimensionalCompartmentUnits | No units defined for 3-D Compartment object | N | N | N | N | N | N | W |
AllowedAttributesOnCompartment | Invalid attribute found on Compartment object | N | N | N | N | N | N | E |
NoUnitsOnCompartment | No units defined for Compartment object | N | N | N | N | N | N | W |
InvalidSpeciesCompartmentRef | Invalid value found for Species 'compartment' attribute | E | E | E | E | E | E | E |
HasOnlySubsNoSpatialUnits | Attribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true' | N | N | E | E | N | N | N |
NoSpatialUnitsInZeroD | Attribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional | N | N | E | E | N | N | N |
NoConcentrationInZeroD | Attribute 'initialConcentration' must not be set if the compartment is zero-dimensional | N | N | E | E | E | E | N |
SpatialUnitsInOneD | Invalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment | N | N | E | E | N | N | N |
SpatialUnitsInTwoD | Invalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment | N | N | E | E | N | N | N |
SpatialUnitsInThreeD | Invalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment | N | N | E | E | N | N | N |
InvalidSpeciesSusbstanceUnits | Invalid value for a Species 'units' attribute | E | E | E | E | E | E | W |
BothAmountAndConcentrationSet | Cannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously | N | N | E | E | E | E | E |
NonBoundarySpeciesAssignedAndUsed | Cannot use a non-boundary species in both reactions and rules simultaneously | W | W | E | E | E | E | E |
NonConstantSpeciesUsed | Cannot use a constant, non-boundary species as a reactant or product | N | N | E | E | E | E | E |
InvalidSpeciesTypeRef | Invalid value for the 'speciesType' attribute of a species | N | N | N | E | E | E | N |
MultSpeciesSameTypeInCompartment | Cannot have multiple species of the same species type in the same compartment | N | N | N | E | E | E | N |
MissingSpeciesCompartment | Missing value for the 'compartment' attribute | E | E | E | E | E | E | E |
SpatialSizeUnitsRemoved | Attribute 'spatialSizeUnits' is not supported in this Level+Version of SBML | N | N | N | N | E | E | N |
SubstanceUnitsOnSpecies | No substance units defined for the species | N | N | N | N | N | N | W |
ConversionFactorOnSpecies | Invalid value for the 'conversionFactor' attribute | N | N | N | N | N | N | E |
AllowedAttributesOnSpecies | Invalid attribute found on Species object | N | N | N | N | N | N | E |
InvalidParameterUnits | Invalid value for the 'units' attribute of a Parameter object | E | E | E | E | E | E | W |
ParameterUnits | No units defined for the parameter | N | N | N | N | N | N | W |
ConversionFactorMustConstant | A conversion factor must reference a Parameter object declared to be a constant | N | N | N | N | N | N | E |
AllowedAttributesOnParameter | Invalid attribute found on Parameter object | N | N | N | N | N | N | E |
InvalidInitAssignSymbol | Invalid value for the 'symbol' attribute of an InitialAssignment object | N | N | N | E | E | E | E |
MultipleInitAssignments | Multiple initial assignments for the same 'symbol' value are not allowed | N | N | N | E | E | E | E |
InitAssignmentAndRuleForSameId | Cannot set a value using both an initial assignment and an assignment rule simultaneously | N | N | N | E | E | E | E |
OneMathElementPerInitialAssign | An InitialAssignment object must contain one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnInitialAssign | Invalid attribute found on an InitialAssignment object | N | N | N | N | N | N | E |
InvalidAssignRuleVariable | Invalid value for the 'variable' attribute of an AssignmentRule object | E | E | E | E | E | E | E |
InvalidRateRuleVariable | Invalid value for the 'variable' attribute of a RateRule object | E | E | E | E | E | E | E |
AssignmentToConstantEntity | An assignment rule cannot assign an entity declared to be constant | N | N | E | E | E | E | E |
RateRuleForConstantEntity | A rate rule cannot assign an entity declared to be constant | N | N | E | E | E | E | E |
CircularRuleDependency | Circular dependencies involving rules and reactions are not permitted | N | N | N | E | E | E | E |
OneMathElementPerRule | A rule object must contain one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnAssignRule | Invalid attribute found on an AssignmentRule object | N | N | N | N | N | N | E |
AllowedAttributesOnRateRule | Invalid attribute found on a RateRule object | N | N | N | N | N | N | E |
AllowedAttributesOnAlgRule | Invalid attribute found on an AlgebraicRule object | N | N | N | N | N | N | E |
ConstraintMathNotBoolean | A Constraint object's <math> must evaluate to a Boolean value | N | N | N | E | E | E | E |
IncorrectOrderInConstraint | Subobjects inside the Constraint object are not in the prescribed order | N | N | N | E | E | E | N |
ConstraintNotInXHTMLNamespace | A Constraint's Message subobject must be in the XHTML XML namespace | N | N | N | E | E | E | N |
ConstraintContainsXMLDecl | XML declarations are not permitted within Constraint's Message objects | N | N | N | E | E | E | E |
ConstraintContainsDOCTYPE | XML DOCTYPE elements are not permitted within Constraint's Message objects | N | N | N | E | E | E | E |
InvalidConstraintContent | Invalid content for a Constraint object's Message object | N | N | N | E | E | E | N |
OneMathElementPerConstraint | A Constraint object must contain one <math> element | N | N | N | N | N | N | E |
OneMessageElementPerConstraint | A Constraint object must contain one Message subobject | N | N | N | N | N | N | E |
AllowedAttributesOnConstraint | Invalid attribute found on Constraint object | N | N | N | N | N | N | E |
NoReactantsOrProducts | Cannot have a reaction with neither reactants nor products | E | E | E | E | E | E | E |
IncorrectOrderInReaction | Subobjects inside the Reaction object are not in the prescribed order | E | E | E | E | E | E | N |
EmptyListInReaction | Reaction components, if present, cannot be empty | E | E | E | E | E | E | E |
InvalidReactantsProductsList | Invalid object found in the list of reactants or products | E | E | E | E | E | E | E |
InvalidModifiersList | Invalid object found in the list of modifiers | N | N | E | E | E | E | E |
OneSubElementPerReaction | A Reaction object can only contain one of each allowed type of object | N | N | N | N | N | N | E |
CompartmentOnReaction | Invalid value for the Reaction 'compartment' attribute | N | N | N | N | N | N | E |
AllowedAttributesOnReaction | Invalid attribute for a Reaction object | N | N | N | N | N | N | E |
InvalidSpeciesReference | Invalid 'species' attribute value in SpeciesReference object | E | E | E | E | E | E | E |
BothStoichiometryAndMath | The 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive | N | N | E | E | E | E | N |
AllowedAttributesOnSpeciesReference | Invalid attribute found on the SpeciesReference object | N | N | N | N | N | N | E |
AllowedAttributesOnModifier | Invalid attribute found on the ModifierSpeciesReference object | N | N | N | N | N | N | E |
UndeclaredSpeciesRef | Unknown species referenced in the kinetic law <math> formula | W | W | E | E | E | E | E |
IncorrectOrderInKineticLaw | Incorrect ordering of components in the KineticLaw object | N | N | E | E | E | E | N |
EmptyListInKineticLaw | The list of parameters, if present, cannot be empty | E | E | E | E | E | E | E |
NonConstantLocalParameter | Parameters local to a KineticLaw object must have a 'constant' attribute value of 'true' | N | N | W | E | E | E | N |
SubsUnitsNoLongerValid | Attribute 'substanceUnits' is not supported in this Level+Version of SBML | N | N | N | E | E | E | N |
TimeUnitsNoLongerValid | Attribute 'timeUnits' is not supported in this Level+Version of SBML | N | N | N | E | E | E | N |
OneListOfPerKineticLaw | Only one ListOfLocalParameters object is permitted within a KineticLaw object | N | N | N | N | N | N | E |
OnlyLocalParamsInListOfLocalParams | Only LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects | N | N | N | N | N | N | E |
AllowedAttributesOnListOfLocalParam | Invalid attribute found on the ListOfLocalParameters object | N | N | N | N | N | N | E |
OneMathPerKineticLaw | Only one <math> element is allowed in a KineticLaw object | N | N | E | E | E | E | E |
UndeclaredSpeciesInStoichMath | Unknown species referenced in the StoichiometryMath object's <math> formula | N | N | W | E | E | E | N |
AllowedAttributesOnKineticLaw | Invalid attribute found on the KineticLaw object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfSpeciesRef | Invalid attribute found on the ListOfSpeciesReferences object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfMods | Invalid attribute found on the ListOfModifiers object | N | N | N | N | N | N | E |
AllowedAttributesOnLocalParameter | Invalid attribute found on the LocalParameter object | N | N | N | N | N | N | E |
MissingTriggerInEvent | The Event object is missing a Trigger subobject | N | N | E | E | E | E | E |
TriggerMathNotBoolean | A Trigger object's <math> expression must evaluate to a Boolean value | N | N | E | E | E | E | E |
MissingEventAssignment | The Event object is missing an EventAssignment subobject | N | N | E | E | E | E | E |
TimeUnitsEvent | Units referenced by 'timeUnits' attribute are not compatible with units of time | N | N | E | E | N | N | N |
IncorrectOrderInEvent | Incorrect ordering of components in Event object | N | N | E | E | E | E | N |
ValuesFromTriggerTimeNeedDelay | Attribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay | N | N | N | N | N | E | N |
DelayNeedsValuesFromTriggerTime | The use of a Delay object requires the Event attribute 'useValuesFromTriggerTime' | N | N | N | N | N | N | N |
OneMathPerTrigger | A Trigger object must have one <math> element | N | N | N | N | N | N | E |
OneMathPerDelay | A Delay object must have one <math> element | N | N | N | N | N | N | E |
InvalidEventAssignmentVariable | Invalid 'variable' attribute value in Event object | N | N | E | E | E | E | E |
EventAssignmentForConstantEntity | An EventAssignment object cannot assign to a component having attribute 'constant'='true' | N | N | W | E | E | E | E |
OneMathPerEventAssignment | An EventAssignment object must have one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnEventAssignment | Invalid attribute found on the EventAssignment object | N | N | N | N | N | N | E |
OnlyOneDelayPerEvent | An Event object can only have one Delay subobject | N | N | N | N | N | N | E |
OneListOfEventAssignmentsPerEvent | An Event object can only have one ListOfEventAssignments subobject | N | N | N | N | N | N | E |
OnlyEventAssignInListOfEventAssign | Only EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments | N | N | N | N | N | N | E |
AllowedAttributesOnListOfEventAssign | Invalid attribute found on the ListOfEventAssignments object | N | N | N | N | N | N | E |
AllowedAttributesOnEvent | Invalid attribute found on the Event object | N | N | N | N | N | N | E |
AllowedAttributesOnTrigger | Invalid attribute found on the Trigger object | N | N | N | N | N | N | E |
AllowedAttributesOnDelay | Invalid attribute found on the Delay object | N | N | N | N | N | N | E |
PersistentNotBoolean | The Trigger attribute 'persistent' must evaluate to a Boolean value | N | N | N | N | N | N | E |
InitialValueNotBoolean | The Trigger attribute 'initialValue' must evaluate to a Boolean value | N | N | N | N | N | N | E |
OnlyOnePriorityPerEvent | An Event object can only have one Priority subobject | N | N | N | N | N | N | E |
OneMathPerPriority | A Priority object must have one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnPriority | Invalid attribute found on the Priority object | N | N | N | N | N | N | E |
GeneralWarningNotSpecified | Unknown error | N | N | N | N | N | N | N |
CompartmentShouldHaveSize | It's best to define a size for every compartment in a model | N | N | W | W | W | W | W |
SpeciesShouldHaveValue | It's best to define an initial amount or initial concentration for every species in a model | N | N | W | W | W | W | W |
ParameterShouldHaveUnits | It's best to declare units for every parameter in a model | W | W | W | W | W | W | W |
LocalParameterShadowsId | Local parameters defined within a kinetic law shadow global object symbols | W | W | W | W | W | W | W |
CannotConvertToL1V1 | Cannot convert to SBML Level 1 Version 1 | N | E | E | E | E | E | E |
NoEventsInL1 | SBML Level 1 does not support events | N | N | E | E | E | E | E |
NoFunctionDefinitionsInL1 | SBML Level 1 does not support function definitions | N | N | W | W | W | W | W |
NoConstraintsInL1 | SBML Level 1 does not support constraints | N | N | N | W | W | W | W |
NoInitialAssignmentsInL1 | SBML Level 1 does not support initial assignments | N | N | N | W | W | W | W |
NoSpeciesTypesInL1 | SBML Level 1 does not support species types | N | N | N | W | W | W | N |
NoCompartmentTypeInL1 | SBML Level 1 does not support compartment types | N | N | N | W | W | W | N |
NoNon3DCompartmentsInL1 | SBML Level 1 only supports three-dimensional compartments | N | N | E | E | E | E | E |
NoFancyStoichiometryMathInL1 | SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas | N | N | E | E | E | E | E |
NoNonIntegerStoichiometryInL1 | SBML Level 1 does not support non-integer 'stoichiometry' attribute values | N | N | E | E | E | E | E |
NoUnitMultipliersOrOffsetsInL1 | SBML Level 1 does not support multipliers or offsets in unit definitions | N | N | E | E | E | E | E |
SpeciesCompartmentRequiredInL1 | In SBML Level 1, a value for 'compartment' is mandatory in species definitions | N | N | E | E | E | E | E |
NoSpeciesSpatialSizeUnitsInL1 | SBML Level 1 does not support species 'spatialSizeUnits' settings | N | N | E | E | E | E | N |
NoSBOTermsInL1 | SBML Level 1 does not support the 'sboTerm' attribute | N | N | N | W | W | W | W |
StrictUnitsRequiredInL1 | SBML Level 1 requires strict unit consistency | N | N | N | N | N | W | W |
ConversionFactorNotInL1 | SBML Level 1 does not support the 'conversionFactor' attribute | N | N | N | N | N | N | E |
CompartmentNotOnL1Reaction | SBML Level 1 does not support the 'compartment' attribute on Reaction objects | N | N | N | N | N | N | W |
ExtentUnitsNotSubstance | Units of extent must be compatible with units of substance | N | N | N | N | N | N | E |
GlobalUnitsNotDeclared | Global units must be refer to unit kind or unitDefinition. | N | N | N | N | N | N | E |
HasOnlySubstanceUnitsNotinL1 | The concept of hasOnlySubstanceUnits was not available in SBML Level 1. | N | N | E | E | E | E | E |
AvogadroNotSupported | Avogadro not supported in Levels 2 and 1. | N | N | N | N | N | N | E |
NoConstraintsInL2v1 | SBML Level 2 Version 1 does not support Constraint objects | N | N | N | W | W | W | W |
NoInitialAssignmentsInL2v1 | SBML Level 2 Version 1 does not support InitialAssignment objects | N | N | N | W | W | W | W |
NoSpeciesTypeInL2v1 | SBML Level 2 Version 1 does not support SpeciesType objects | N | N | N | W | W | W | N |
NoCompartmentTypeInL2v1 | SBML Level 2 Version 1 does not support CompartmentType objects | N | N | N | W | W | W | N |
NoSBOTermsInL2v1 | SBML Level 2 Version 1 does not support the 'sboTerm' attribute | N | N | N | W | W | W | W |
NoIdOnSpeciesReferenceInL2v1 | SBML Level 2 Version 1 does not support the 'id' attribute on SpeciesReference objects | N | N | N | W | W | W | W |
NoDelayedEventAssignmentInL2v1 | SBML Level 2 Version 1 does not support the 'useValuesFromTriggerTime' attribute | N | N | N | N | N | E | E |
StrictUnitsRequiredInL2v1 | SBML Level 2 Version 1 requires strict unit consistency | N | N | N | N | N | W | W |
IntegerSpatialDimensions | SBML Level 2 Version 1 requires that compartments have spatial dimensions of 0-3 | N | N | N | N | N | N | E |
StoichiometryMathNotYetSupported | Conversion to StoichiometryMath objects not yet supported | N | N | N | N | N | N | N |
PriorityLostFromL3 | SBML Level 2 Version 1 does not support priorities on Event objects | N | N | N | N | N | N | E |
NonPersistentNotSupported | SBML Level 2 Version 1 does not support the 'persistent' attribute on Trigger objects | N | N | N | N | N | N | E |
InitialValueFalseEventNotSupported | SBML Level 2 Version 1 does not support the 'initialValue' attribute on Trigger objects | N | N | N | N | N | N | E |
SBOTermNotUniversalInL2v2 | The 'sboTerm' attribute is invalid for this component in SBML Level 2 Version 2 | N | N | N | N | W | W | W |
NoUnitOffsetInL2v2 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL2v2 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL2v2 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoDelayedEventAssignmentInL2v2 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute | N | N | N | N | N | E | E |
ModelSBOBranchChangedBeyondL2v2 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | N | N | E | E |
StrictUnitsRequiredInL2v2 | SBML Level 2 Version 2 requires strict unit consistency | N | N | N | N | N | W | W |
StrictSBORequiredInL2v2 | SBML Level 2 Version 2 requires strict SBO term consistency | N | N | N | N | N | W | W |
DuplicateAnnotationInvalidInL2v2 | Duplicate top-level annotations are invalid in SBML Level 2 Version 2 | W | W | W | N | N | N | N |
NoUnitOffsetInL2v3 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL2v3 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoSpeciesSpatialSizeUnitsInL2v3 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | N | N | E | E | N | N | N |
NoEventTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | E | E | N | N | N |
NoDelayedEventAssignmentInL2v3 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute | N | N | N | N | N | E | E |
ModelSBOBranchChangedBeyondL2v3 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | N | N | E | E |
StrictUnitsRequiredInL2v3 | SBML Level 2 Version 3 requires strict unit consistency | N | N | N | N | N | W | W |
StrictSBORequiredInL2v3 | SBML Level 2 Version 3 requires strict SBO term consistency | N | N | N | N | N | W | W |
DuplicateAnnotationInvalidInL2v3 | Duplicate top-level annotations are invalid in SBML Level 2 Version 3 | W | W | W | N | N | N | N |
NoUnitOffsetInL2v4 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL2v4 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoSpeciesSpatialSizeUnitsInL2v4 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | N | N | E | E | N | N | N |
NoEventTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | E | E | N | N | N |
ModelSBOBranchChangedInL2v4 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | E | E | N | N |
DuplicateAnnotationInvalidInL2v4 | Duplicate top-level annotations are invalid in SBML Level 2 Version 4 | W | W | W | N | N | N | N |
NoSpeciesTypeInL3v1 | SBML Level 3 Version 1 does not support SpeciesType objects | N | N | N | W | W | W | N |
NoCompartmentTypeInL3v1 | SBML Level 3 Version 1 does not support CompartmentType objects | N | N | N | W | W | W | N |
NoUnitOffsetInL3v1 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL3v1 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoSpeciesSpatialSizeUnitsInL3v1 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | N | N | E | E | N | N | N |
NoEventTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | E | E | N | N | N |
ModelSBOBranchChangedInL3v1 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | E | E | N | N |
DuplicateAnnotationInvalidInL3v1 | Duplicate top-level annotations are invalid in SBML Level 3 Version 1 | W | W | W | N | N | N | N |
NoCompartmentOutsideInL3v1 | This Level+Version of SBML does not support the 'outside' attribute on Compartment objects | W | W | W | W | W | W | N |
NoStoichiometryMathInL3v1 | This Level+Version of SBML does not support the StoichiometryMath object | N | N | E | E | E | E | N |
InvalidSBMLLevelVersion | Unknown Level+Version combination of SBML | E | E | E | E | E | E | E |
AnnotationNotesNotAllowedLevel1 | Annotation objects on the SBML container element are not permitted in SBML Level 1 | E | E | N | N | N | N | N |
InvalidRuleOrdering | Invalid ordering of rules | E | E | E | N | N | N | N |
RequiredPackagePresent | The SBML document requires an SBML Level 3 package unavailable in this software | N | N | N | N | N | N | E |
UnrequiredPackagePresent | The SBML document uses an SBML Level 3 package unavailable in this software | N | N | N | N | N | N | W |
PackageRequiredShouldBeFalse | This package expects required to be false. | N | N | N | N | N | N | W |
SubsUnitsAllowedInKL | Disallowed value for attribute 'substanceUnits' on KineticLaw object | E | E | E | N | N | N | N |
TimeUnitsAllowedInKL | Disallowed value for attribute 'timeUnits' on KineticLaw object | E | E | E | N | N | N | N |
FormulaInLevel1KL | Only predefined functions are allowed in SBML Level 1 formulas | E | E | N | N | N | N | N |
L3SubstanceUnitsOnModel | Invalid 'substanceUnits' attribute value | N | N | N | N | N | N | W |
TimeUnitsRemoved | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | N | N | E | E | E |
BadMathML | Invalid MathML expression | N | N | E | E | E | E | E |
FailedMathMLReadOfDouble | Missing or invalid floating-point number in MathML expression | N | N | E | E | E | E | E |
FailedMathMLReadOfInteger | Missing or invalid integer in MathML expression | N | N | E | E | E | E | E |
FailedMathMLReadOfExponential | Missing or invalid exponential expression in MathML | N | N | E | E | E | E | E |
FailedMathMLReadOfRational | Missing or invalid rational expression in MathML | N | N | E | E | E | E | E |
BadMathMLNodeType | Invalid MathML element | N | N | E | E | E | E | E |
NoTimeSymbolInFunctionDef | Use of <csymbol> for 'time' not allowed within FunctionDefinition objects | N | N | W | E | E | E | E |
NoBodyInFunctionDef | There must be a <lambda> body within the <math> element of a FunctionDefinition object | N | N | E | E | E | E | E |
DanglingUnitSIdRef | Units must refer to valid unit or unitDefinition | W | W | W | W | W | W | W |
RDFMissingAboutTag | RDF missing the <about> tag. | N | N | N | W | W | W | W |
RDFEmptyAboutTag | RDF empty <about> tag. | N | N | N | W | W | W | W |
RDFAboutTagNotMetaid | RDF <about> tag is not metaid. | N | N | N | W | W | W | W |
RDFNotCompleteModelHistory | RDF does not contain valid ModelHistory. | N | N | N | W | W | W | W |
RDFNotModelHistory | RDF does not result in a ModelHistory. | N | N | N | W | W | W | W |
AnnotationNotElement | Annotation must contain element. | N | N | N | W | W | W | W |
UndeclaredUnits | Missing unit declarations on parameters or literal numbers in expression | W | W | W | W | W | W | W |
UndeclaredTimeUnitsL3 | Unable to verify consistency of units: the unit of time has not been declared | N | N | N | N | N | N | W |
UndeclaredExtentUnitsL3 | Unable to verify consistency of units: the units of reaction extent have not been declared | N | N | N | N | N | N | W |
UndeclaredObjectUnitsL3 | Unable to verify consistency of units: encountered a model entity with no declared units | N | N | N | N | N | N | W |
UnrecognisedSBOTerm | Unrecognized 'sboTerm' attribute value | N | N | N | W | W | W | W |
ObseleteSBOTerm | Obsolete 'sboTerm' attribute value | N | N | N | W | W | W | W |
IncorrectCompartmentSpatialDimensions | In SBML Level 1, only three-dimensional compartments are allowed | E | E | N | N | N | N | N |
CompartmentTypeNotValidAttribute | CompartmentType objects are not available in this Level+Version of SBML | E | E | E | N | N | N | E |
ConstantNotValidAttribute | This Level+Version of SBML does not support the 'constant' attribute on this component | E | E | N | N | N | N | N |
MetaIdNotValidAttribute | Attribute 'metaid' is not available in SBML Level 1 | E | E | N | N | N | N | N |
SBOTermNotValidAttributeBeforeL2V3 | The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3 | E | E | E | E | N | N | N |
InvalidL1CompartmentUnits | Invalid units for a compartment in SBML Level 1 | E | E | N | N | N | N | N |
L1V1CompartmentVolumeReqd | In SBML Level 1, a compartment's volume must be specified | E | N | N | N | N | N | N |
CompartmentTypeNotValidComponent | CompartmentType objects are not available in this Level+Version of SBML | E | E | E | N | N | N | E |
ConstraintNotValidComponent | Constraint objects are not available in this Level+Version of SBML | E | E | E | N | N | N | N |
EventNotValidComponent | Event objects are not available in this Level+Version of SBML | E | E | N | N | N | N | N |
SBOTermNotValidAttributeBeforeL2V2 | The 'sboTerm' attribute is invalid for this component before Level 2 Version 2 | E | E | E | N | N | N | N |
FuncDefNotValidComponent | FunctionDefinition objects are not available in this Level+Version of SBML | E | E | N | N | N | N | N |
InitialAssignNotValidComponent | InitialAssignment objects are not available in this Level+Version of SBML | E | E | E | N | N | N | N |
VariableNotValidAttribute | Attribute 'variable' is not available on this component in this Level+Version of SBML | E | E | E | E | E | E | E |
UnitsNotValidAttribute | Attribute 'units' is not available on this component in this Level+Version of SBML | E | E | E | E | E | E | E |
ConstantSpeciesNotValidAttribute | Attribute 'constant' is not available on Species objects in SBML Level 1 | E | E | N | N | N | N | N |
SpatialSizeUnitsNotValidAttribute | Attribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1 | E | E | N | N | N | N | N |
SpeciesTypeNotValidAttribute | Attribute 'speciesType' is not available on Species objects in SBML Level 1 | E | E | E | N | N | N | E |
HasOnlySubsUnitsNotValidAttribute | Attribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1 | E | E | N | N | N | N | N |
IdNotValidAttribute | Attribute 'id' is not available on SpeciesReference objects in SBML Level 1 | E | E | E | N | N | N | N |
NameNotValidAttribute | Attribute 'name' is not available on SpeciesReference objects in SBML Level 1 | E | E | E | N | N | N | N |
SpeciesTypeNotValidComponent | The SpeciesType object is not supported in SBML Level 1 | E | E | E | N | N | N | E |
StoichiometryMathNotValidComponent | The StoichiometryMath object is not supported in SBML Level 1 | E | E | N | N | N | N | E |
MultiplierNotValidAttribute | Attribute 'multiplier' on Unit objects is not supported in SBML Level 1 | E | E | N | N | N | N | N |
OffsetNotValidAttribute | Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1 | E | E | N | N | N | N | N |
L3SpatialDimensionsUnset | No value given for 'spatialDimensions' attribute; assuming a value of 3 | N | N | N | N | N | N | W |
PackageConversionNotSupported | Conversion of SBML Level 3 package constructs is not yet supported | E | E | E | E | E | E | E |
InvalidTargetLevelVersion | The requested SBML Level/Version combination is not known to exist | E | E | E | E | E | E | E |
L3NotSupported | SBML Level 3 is not yet supported | E | E | E | E | E | E | E |
Enumerator | Meaning |
---|---|
LIBSBML_CAT_SBML | General 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 Version 1 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 Version 1 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 Version 1 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 Version 1 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 Version 1 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 Version 1 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. |