The following errors are generated by the SBML importer and exporter. If you encounter errors related to SBML import, please check your SBML file with the SBML On-line Validator at http://sbml.org/tools/htdocs/sbmltools.php before you file a bug report.
Identifier
SBML (1)
Message
SBML Level 2 Version 1 does not support initial times different from 0. This information will be lost in the exported file.
Description
The initial time of your model is set to a value different than 0. This information can not be stored in SBML Level2 Version1 and will therefore not be present in the exported model.
Identifier
SBML (2)
Message
The SBML document contains no model.
Description
This error occurs if you try to load an SBML file that does not contain a model.
Identifier
SBML (3)
Message
The SBML document contains algebraic rules that were ignored. Entities determined by those rules are probably undetermined now.
Description
COPASI does not support SBML algebraic rules yet, so if you load an SBML file that contains algebraic rules, COPASI will warn you that the rules have been ignored. Please be aware that this will very likely change simulation results.
Identifier
SBML (4)
Message
The SBML document contains events that were ignored.
Description
COPASI does not support SBML events yet, so if you load an SBML file that contains events, COPASI will warn you that the events have been ignored. Please be aware that this will very likely change simulation results.
Identifier
SBML (5)
Message
Compartment COMPARTMENTID referenced by species SPECIESID does not exist.
Description
In the SBML file a the species with id SPECIESID references the compartment with id COMPARTMENTID, but a compartment with this id does not exist.
Identifier
SBML (6)
Message
Annotations in SBase element of SBML Level 1 files, this is invalid and has been ignored.
Description
Some programs add annotations to the SBase element of the file which is incorrect. Since it doesn't affect the mode, COPASI reads the model anyway but ignores the annotation. If you want to keep the annotation please open the SBML file in a text editor and move it to e.g. the model element.
Identifier
SBML (7)
Message
No initial value or initial assignment set for compartment "COMPARTMENTID".
Description
In order to simulate a model in COPASI it has to be complete, meaning all initial values (or, initial assignment) and parameter values have to be set. SBML allows the user to specify incomplete models. This warning tells the user that some values in the model have not been set and that the model is incomplete. Most tasks in COPASI will not work with this model until all values have been set. Unset values will be shown as NaN in COPASI graphical user interface. The fastest way to find unset values is to use the . This warning can also be the result of an ignored rule that would normally set the value of this model entity.
Identifier
SBML (8)
Message
Expression tree for kinetic law of reaction 'REACTIONID' could not be converted.
Description
The kinetic formula for the reaction with id REACTIONID could not be converted into COPASI's internal function representation. If you think the formula is correct, please send as a bug report with the SBML file included so we can have a look at it.
Identifier
SBML (9)
Message
Could not set function from expression in reaction 'REACTIONID'.
Description
Somehow COPASI was able to generate in internal representation for a function formula, but could not use it with a reaction. If you get such an error, please send as a bug report with the SBML file so we can look at it.
Identifier
SBML (11)
Message
Function 'FUNCTIONID' does not start with a Lambda element.
Description
Function definitions in MathML have to start with a Lambda element. If you see this error, the function with the id FUNCTIONID is very likely incorrect MathML because it is missing this element.
Identifier
SBML (12)
Message
Function 'FUNCTIONID' contains invalid parameter list.
Description
The error message means that the parameter list for the function definition with id FUNCTIONID contains an invalid type, e.g. a number instead of a parameter name.
Identifier
SBML (13)
Message
Could not read function definition for function 'FUNCTIONID'.
Description
COPASI could not read the function definition with id FUNCTIONID. If you think this function definition is correct, please send us a bug report and include the SBML file.
Identifier
SBML (14)
Message
Could not import function with id 'ID'.
Description
This error message is very similar to the one above but the error here already occurred in libsbml while reading the function definition.
Identifier
SBML (15)
Message
Could not find function with id 'ID'.
Description
COPASI could not find the function with id ID while exporting a model to SBML. If you get this error message please save the model as a COPASI file and send us a bug report with this file.
Identifier
SBML (16)
Message
Loop found in function. That means a function calls itself either directly or indirectly.
Description
COPASI has found a loop in a function call while exporting your model to SBML. This should never happen so if you see this error message please save the model as a COPASI file and send us a bug report with this file.
Identifier
SBML (17)
Message
One or more single compartment reactions found where the kinetic law does not include a multiplication by the volume: REACTIONID.
Description
This is a warning only. Please see the COPASI FAQ question 'Why are some rate laws in SBML files exported by COPASI multiplied by the compartment volume?' at http://www.copasi.org/. If COPASI finds a species reference in a reaction that has the hasOnlySubstanceUnits flag set, the warning is not generated for that reaction.
Identifier
SBML (18)
Message
Support for 'hasOnlySubstanceUnit' flag on species is experimental. Species in compartments of dimension 0 are also considered to have this flag set.
Description
Dealing with species in SBML files that have the "hasOnlySubstanceUnits" flag set has changed in recent versions of COPASI. We are pretty sure that the way it is handled now is correct. If you think that you found a case where COPASI does it incorrectly, please let us know.
Identifier
SBML (19)
Message
Spatial size units on species "SPECIESID" is not the same as the volume unit in the model and has been ignored.
Description
COPASI does not support the spatialSizeUnits attribute for species. The species with id SPECIESID in the current file seems to use this attribute however.
Identifier
SBML (20)
Message
Setting an initial concentration on species SPECIESID which has the 'hasOnlySubstanceUnits' flag set is not allowed.
Description
The SBML file seems to contain a species with id SPECIESID that has the hasOnlySubstanceUnits flag set to true but also has an initialConcentration set. This is incorrect, please specify an initial amount instead.
Identifier
SBML (21)
Message
Setting an initial concentration on species 'SPECIESID' which is in a compartment with spatial dimensions 0 is not allowed.
Description
Having a compartment with a spatial dimension of 0 implies that all species within this compartment have the hasOnlySubstanceUnits flag set to true. Therefore it is incorrect to specify an initial concentration for those species. Specify an initial amount instead. Current version of COPASI refuse to read models with compartments that have their spatial size units set to 0 so this error message will never appear.
Identifier
SBML (22)
Message
Current versions of COPASI only supports three dimensional compartments. 'COMPARTMENTID' will be converted to be three dimensions.
Description
COPASI only supports three dimensional compartments so far, so all compartments are converted to three dimensions no matter what is specified in the SBML file. Independent of this is the handling of spatial dimensions that are set to 0 in the SBML file (see error SBML (21) above). Current version of COPASI refuse to read models with compartments that have their spatial size units set to 0 so this error message will never appear.
Identifier
SBML (23)
Message
Compartment 'COMPARTMENTID' has spatial dimensions of 0, setting dimensions to 3. Considering all species in that compartment to have "hasOnlySubstanceUnits" flag set.
Description
If the compartment in an SBML file has a spatial dimension of 0, all species in the compartment are considered to have the "hasOnlySpeciesUnits" flag set. This means that if such a species is referenced within a mathematical expression, the amount of the species is referenced and not the concentration. Since COPASI only knows threedimensional compartments, the dimensionality of the compartment is ignored, this can lead to incorrect display of units within COPASI, but it should not affect numerical values of the kodel of of calculations done on the model Since COPASI only knows threedimensional compartments, the dimensionality of the compartment is ignored, this can lead to incorrect display of units within COPASI, but it should not affect numerical values of the kodel of of calculations done on the model.
Identifier
SBML (24)
Message
Units for some compartments were ignored. Units might be displayed incorrectly. Compartments: COMPARTMENTSID.
Description
If COPASI finds a compartment that has units different from the default volume units of the model, the units are ignored. This might lead to the display of incorrect units in the GUI.
Identifier
SBML (25)
Message
Units for some species were ignored. Units might be displayed incorrectly. Species: SPECIESID.
Description
If COPASI finds a species that has units different from the default substance units of the model, the units are ignored. This might lead to the display of incorrect units in the GUI.
Identifier
SBML (26)
Message
Units for some parameters were ignored. Units might be displayed incorrectly. Parameters: PARAMETERSID.
Description
If COPASI finds a parameter that has units set, the units are ignored. This might lead to the display of incorrect units in the GUI.
Identifier
SBML (27)
Message
Error in kinetic law for reaction 'REACTIONID'.
Description
Some error occurred while creating the kinetic law for the reaction with id REACTIONID. If you think the kinetic law in the SBML file is OK, please send a bug report and include the SBML file so that we can have a look at it.
Identifier
SBML (28)
Message
Error in function definition with id 'ID'.
Description
Somehow COPASI was not able to convert the function definition with id ID into it's internal format. If you think the function definition is correct, please send a bug report and include the SBML file.
Identifier
SBML (29)
Message
Unable to handle reactions with the 'fast' flag set. The flag has been set to false.
Description
COPASI is not yet able to handle reactions that are set to fast correctly the flag will be automatically set to false on import. In some cases simulation results for these models can be incorrect.
Identifier
SBML (30)
Message
Can't handle units of type item with scale set to 1. If this file was created with COPASI RC1 or older please see the COPASI FAQ.
Description
COPASI prior to and including RC1 had a bug in the SBML exporter. If the default concentration units were set to items, COPASI would set the scale to 1 instead of 0 on the exported substance unit definition. You can correct those files by opening them in a text editor and setting the scale for the substance units to 0. If the file was not created with COPASI, the scale was probably meant to be 1 and COPASI can not import it since it does not do unit conversion yet.
Identifier
SBML (31)
Message
Assigment/ODE-Rules are currently only supported for global parameters.
Description
(OBSOLETE) COPASI currently only supports assignment and ODE rules for global parameters, if an SBML file contains such rules for species or compartments, they are ignored. Working with such a model in COPASI will most likely lead to incorrect results.
Identifier
SBML (32)
Message
Error in Assignment/ODE-Rule's variable id 'ID' does not specify a compartment, species or global parameter.
Description
Rules in SBML files are only allowed on compartments, species and global parameters if the id referenced from a rule does not correspond to one of those entity types, it is an error.
Identifier
SBML (33)
Message
Error: Assignment/ODE-Rule is not allowed for local parameter 'PARAMETERID'.
Description
COPASI encountered a rule for a local parameter which is not allowed.
Identifier
SBML (34)
Message
Error: Assignment/ODE-Rule is not allowed for local constant 'CONSTANTNAME' identified by id 'ID'
Description
~!!!UNDOCUMENTED!!!
Identifier
SBML (35)
Message
Error: Only one AssignmentRule or RateRule is allowed for id 'ID'.
Description
COPASI has encountered an entity for which more than one rule has been specified.
Identifier
SBML (36)
Message
COPASI does not support time delays. Calculations on this model will most likely lead to unusable results.
Description
COPASI currently does has no possibility to calculate time delays as they are supported in SBML models. If COPASI encounters a model with such a time delay, the delay is converted to a normal function call that evaluates to NaN (Not a number). This might lead to calculation results containing a large amount of NaN values instead of numerical values. If you want to work with the model, you have to remove all calls to the delay function from the mathematical expressions in the model.
Identifier
SBML (37)
Message
The id 'ID' is used in the expression of a rule, although it is later defined by a rule itself.
Description
An object is referenced in the expression of a rule but is later defined by a rule itself. This is not allowed, please change the order of rules in the SBML file so that the rule for object with id is listed before the rule ID is referenced in. Also make sure that this does not lead to circular dependencies.
Identifier
SBML (38)
Message
Only references to compartment volumes, species concentrations, global parameter values or the time are allowed in SBML rule expressions.
Description
Objects referenced from the expression of a rule in SBML can only be compartments, species or global parameters.
Identifier
SBML (39)
Message
Object with id "ID" referenced in kinetic law, but no object with that id found in model.
Description
An id is referenced in the expression of a kinetic law, but COPASI could not find an object with that id in the model.
Identifier
SBML (40)
Message
LIBSBML ERRORTYPE ERRORNUMBER at line LINENUMBER column COLUMNNUMBER: ERRORMESSAGE.
Description
This error message actually encapsulates all errors, informations and warnings libSBML finds while checking a file it loads. The error message will tell you the severity of the message, the error number, where it occured in the file and the actual message from libSBML. Right now libSBML will probably give you many warnings and errors for your files which you can either ignore or depending on the error, use to fix the model file. If you think that an error message is actually incorrect, please let the authors of libSBML know so that they can have a look at it.
Identifier
SBML (41)
Message
No initial value set for species "SPECIESID". Setting initial concentration to 1.0.
Description
In order to simulate a model in COPASI it has to be complete, meaning all initial values and parameter values have to be set. SBML allows the user to specify incomplete models. This warning tells the user that some values in the model have not been set and that the model is incomplete. Most tasks in COPASI will not work with this model until all values have been set. Unset values will be shown as NaN in COPASI graphical user interface. It is save to set the initial concentration to 1.0.
Identifier
SBML (42)
Message
No initial value set for local parameter "PARAMETERID".
Description
In order to simulate a model in COPASI it has to be complete, meaning all initial values and parameter values have to be set. SBML allows the user to specify incomplete models. This warning tells the user that some values in the model have not been set and that the model is incomplete. Most tasks in COPASI will not work with this model until all values have been set. Unset values will be shown as NaN in COPASI graphical user interface. The fastest way to find unset values is to use the . This warning can also be the result of an ignored rule that would normally set the value of this model entity.
Identifier
SBML (43)
Message
No initial value set for global parameter "PARAMETERID".
Description
In order to simulate a model in COPASI it has to be complete, meaning all initial values and parameter values have to be set. SBML allows the user to specify incomplete models. This warning tells the user that some values in the model have not been set and that the model is incomplete. Most tasks in COPASI will not work with this model until all values have been set. Unset values will be shown as NaN in COPASI graphical user interface. The fastest way to find unset values is to use the . This warning can also be the result of an ignored rule that would normally set the value of this model entity.
Identifier
SBML (44)
Message
Substance unit in kinetic law for some reactions were ignored. Units might be displayed incorrectly. Reactions: REACTIONSID.
Description
If COPASI finds substance units in a kinetic law that differ from the default substance units of the model, those units are ignored. This might lead to the display of incorrect units in the GUI.
Identifier
SBML (45)
Message
Compartment "COMPARTMENTID" does not set the initial volume. Volume has been set to 1.0.
Description
COPASI has found a compartment in the model that does not specify an initial volume. Since COPASI needs this information, it would normally not be able to read those models. In certain cases when all species of the compartment in question have the hasOnylSubstanceUnits flag set, it is save to set the volume of that compartment to 1.0 in order to be able to read the model.
Identifier
SBML (46)
Message
COPASI has changed the following function definitions to take the time as an additional argument instead of the function being directly or indirectly dependent on time: "FUNCTIONNAME" .
Description
Up to SBML Level 2 Version 2 it was legal to use the time symbol within a function definition. Since COPASI can not ahndle this internally, those function definitions have to be converted to take an extra parameter which is the time. All appearances of the time symbol within the function definition are replaced by the name of the parameter. COPASI also replaces all function calls to those functions by new function calls that have the extra parameter which corresponds to time. Since starting with SBML Level 2 Version 3 it is illegal to have a time object in a function definition, this also helps to generate SBML files that are easily converted to future versions.
Identifier
SBML (47)
Message
COPASI found a call to the function "FUNCTIONID" which has not been defined.
Description
In some MathML term in the SBML file, COPASI found a term that is used as a function, but where it does not correspond to a predefined MathML function or the id of any function definition in the file.
Identifier
SBML (49)
Message
Constraints ignored because they are not supported yet.
Description
The current versions of COPASI do not support SBML constraints yet. We hope to change this in the future.
Identifier
SBML (50)
Message
Could not open file "FILENAME".
Description
Out of some reason, COPASI could not open the file. Reasons for this can be for example that the file does not exist, the user does not have sufficient permissions to open the file or that the file isn't an SBML file.
Identifier
SBML (51)
Message
The species "SPECIESID" is defined by a rate rule and its compartments volume is variable. COPASI will probably interpret this incorrectly.
Description
COPASIs interpretation of species that are defined by a rate rule and that are located in a non-constant compartment differes slightly from the interpretation intended by the SBML specification. This difference might lead to calculation results that are not consistent with the given SBML file. We hope to fix this in future version of COPASI.
Identifier
SBML (52)
Message
The species "SPECIESID" is defined by a rate expression and its compartments volume is variable. The way COPASI interprets this is differently from the way SBML does.
Description
COPASIs interpretation of species that are defined by a rate rule and that are located in a non-constant compartment differes slightly from the interpretation intended by the SBML specification. If such a model is exported to SBML, the resulting SBML model is not identical to the original COPASI model. We hope to fix this in future versions of COPASI.
Identifier
SBML (53)
Message
The time units of kinetic laws in some reactions were ignored. Units might be displayed incorrectly. Reactions: REACTIONSID.
Description
If COPASI finds a kinetic law in an SBL file that has time units different from the global time units, they are ignored. This might lead to incorrect units being displayed in the GUI.
Identifier
SBML (54)
Message
Error while importing volume unit with id "ID".
Description
COPASI could not convert the given volume unit to one of its own volume units. This might lead to incorrect units being displayed in the GUI.
Identifier
SBML (55)
Message
Could not find unit definition for unit with id "ID" used in "ATTRIBUTE" attribute of UNIT with id "ID".
Description
COPASI found a reference to a unit definition that has not been defined in the file.
Identifier
SBML (56)
Message
There was a problem with the kinetic law in reaction "REACTIONSID". Make sure the math element is not empty.
Description
Out of some reason COPASI could not import the kinetic law of some reaction. Most often this means that the kinetic law has some error. If you think that the kinetic law is correct, please send us a bug report.
Identifier
SBML (57)
Message
InitialAssignment defined for object with id "ID", but the corresponding object could not be found. Ignoring assignment.
Description
The SBML file contains an initial assignment for an object that is not defined in the SBML file.
Identifier
SBML (58)
Message
InitialAssignment for object with id "ID" does not set a mathematical expression. Ignoring assignment.
Description
The SBML file contains an initial assignment that does not define a mathematical expression for the assignment.
Identifier
SBML (59)
Message
Error while importing InitialAssignment for object with id "ID". Ignoring assignment.
Description
If this error message comes up, the initial assignment is incorrect, or you have found a bug in COPASI. If you think the initial assignment is actually correct, please send us a bug report.
Identifier
SBML (60)
Message
Error while exporting EXPRESSIONTYPE for ELEMENTTYPE with name "ELEMENTNAME".
Description
This error means that there were problems when exporting a rule or an initial assignment. If you see this message, it is very likely that you have found a bug in COPASI. Please send us a bug report that includes the COPASI file for reproducing this error.
Identifier
SBML (61)
Message
Error while expanding function calls in mathematical expression for EXPRESSIONID.
Description
This error means that there were problems when exporting a mathematical expression the SBML Level 1. If you see this message, it is very likely that you have found a bug in COPASI. Please send us a bug report that includes the COPASI file for reproducing this error.
Identifier
SBML (62)
Message
Error while replacing unsupported elements in mathematical expression for EXPRESSIONID.
Description
This error means that there were problems when exporting a mathematical expression the SBML Level 1. Either the expression that was exported contained elements that could not be represented in SBML Level 1, or you have found a bug in COPASI. Since exporting to SBML Level 1 is a new feature, it would be nice, if you could provide us with a bug report if you see this message.
Identifier
SBML (63)
Message
Initial assignment for ASSIGNMENTID "ASSIGNMENT" can not be exported to SBML Level 2 Version 1.
Description
Initial assignment have been introduced in SBML Level 2 Version 2, so models that contain initial assignments can not be exporter to SBML Level 2 Version 1.
Identifier
SBML (64)
Message
One or more stoichiometric expressions were evaluated and converted to constants values.
Description
COPASI does not support stoichiometric expression, so when an SBML file contains a stoichiometric expression, the expression is evaluated and converted to a constant. This will lead to incorrect calculation results if the expression contained a variable element.
Identifier
SBML (65)
Message
The stoichiometric expression for a species reference for species "SPECIESID" in reaction "REACTIONID" could not be evaluated. The value has therefore been set to 1.0..
Description
COPASI was not able to evaluate the stoichiometric expression for some species reference. This either means that the expression was incorrect, or that you found a bug in COPASI. If you think that the expression is correct, please sned us a bug report.
Identifier
SBML (66)
Message
COPASI was not able to import the global UNITTYPE unit. Unit has been set to UNIT.
Description
This error means that COPASI has encountered some problem while importing one of the global units for either substance, time or volume. Most likely this is due to the fact that the unit in the SBML file could not be converted to a unit COPASI understands. The corresponding unit has therefore been set to a default unit. As a consequence, the units displayed in the GUI might be incorrect. It has however no influence on any calculations with the model or the numerical values generated during those calculations.
