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Systems Biology Markup Language (SBML)

Tracker: libSBML




Welcome to the issue reporting system for libSBML

This is the public issue reporting system for libSBML, a portable library for reading, writing and manipulating SBML files and data streams. Users are invited to report issues (such as problems, lack of clarity in the documentation, missing functionality, etc.) using this system for any version of libSBML.

Click here to report a libSBML issue or request a new feature.

Reported issues are reviewed and evaluated by the libSBML developers, then acted upon, and actions taken are logged with the reported issue in this system. Once actions on a given issue are concluded, the issue is marked as "closed" in this system, but it is never deleted and its record can always be accessed.



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ID Summary Status Opened Assignee Submitter Priority
ID Summary Status Opened Assignee Submitter Priority
Assignee: Status: Category: Group: Submitter: Keyword: Artifact ID: Permalink
2946870 setLevelAndVersion not working Open 2010-02-05 nobody luciansmith 5
2943189 Error in Matlab binding 2009a / OSX 10.6 Closed 2010-01-31 nobody kieransmallbone 5
2939833 Java .jar file not actually in /usr/local/lib/ Open 2010-01-25 mhuckaSourceForge.net DonorProject Admin luciansmith 5
2937584 'configure --with-java' not enough? Maybe? Open 2010-01-23 nobody luciansmith 5
2929911 Segmentation Fault Error (using Python Bindings) Closed 2010-01-11 nobody https://www.google.com/accounts 5
2910508 binding matlab with lisSBML for windows Open 2009-12-08 nobody nobody 5
2903961 SBMLError::getShortMessage sometimes returning empty string Closed 2009-11-25 nobody fbergmann 5
2897563 Problem with eventID Open 2009-11-14 nobody nobody 5
2895082 Build error with Matlab R2009a and Ubuntu 9.10 64 bit Closed 2009-11-10 nobody nobody 5
2879118 Doing bad things with the converter Open 2009-10-14 nobody luciansmith 5
2878770 check unique metaid Closed 2009-10-14 nobody sarahkeatingProject Admin 5
2878106 back-converting models with inconsistent units Open 2009-10-13 nobody luciansmith 3
2877381 'issetstoichiometry' makes biomodels40 fail Closed 2009-10-12 ajourakuProject Admin luciansmith 5
2877188 'setLevelAndVersion' not documented? Open 2009-10-12 mhuckaSourceForge.net DonorProject Admin luciansmith 5
2877180 Can you add 'readSBMLFromFile'? Closed 2009-10-12 nobody luciansmith 5
2877178 SBMLDocuments with changed levels/versions fail XML check Deleted 2009-10-12 nobody luciansmith 5
2873623 renaming elements Open 2009-10-06 nobody fbergmann 5
2873484 segmentation violation when validating in matlab Closed 2009-10-06 sarahkeatingProject Admin bheavner 5
2870222 --with-zlib=no ignored; compile fails Closed 2009-09-29 nobody luciansmith 5
2865376 SBMLDocument constructor fails valgrind Closed 2009-09-23 nobody luciansmith 5
2865288 Build error with Matlab R2009a and CentOS 5.3 64bit Closed 2009-09-23 nobody nobody 5
2859186 Inconsistent unit checks Closed 2009-09-15 nobody sarahkeatingProject Admin 5
2856390 Disappearing events Closed 2009-09-10 nobody luciansmith 5
2855781 memory leak from SBMLDocument::checkConsistency() Closed 2009-09-10 nobody nobody 5
2848262 Forgotten bracket in documentation of SBMLdocument Open 2009-09-01 mhuckaSourceForge.net DonorProject Admin nobody 5
2842277 SBML_formulaToString(...) returns a non-owning pointer Open 2009-08-21 nobody luciansmith 3
2840693 Inexplicable leaks when reading SBML from stream not char* Closed 2009-08-20 nobody luciansmith 5
2840685 libsbml includes turn on 'use namespace std' Closed 2009-08-19 nobody luciansmith 5
2839173 Error messages from incorrectly setting 'notes' Open 2009-08-17 nobody luciansmith 3
2837191 Model validation can crash with illogical ASTNode Closed 2009-08-13 nobody nobody 5
2835929 elements currently support setSBOTerm(int) but not the Id Closed 2009-08-12 ajourakuProject Admin fbergmann 5
2835239 accessing definition URLs of ci elements not possible ... Closed 2009-08-10 nobody fbergmann 5
2835101 conversion of MathML to infix problem Closed 2009-08-10 nobody fbergmann 5
2829608 Segmentation Fault using getListOfReactions Open 2009-07-30 nobody linsson 5
2818945 incorrect documentation for getDerivedUnitDefinition Closed 2009-07-09 mhuckaSourceForge.net DonorProject Admin gauges 5
2818943 bug in copy constructor of FormulaDataUnits Closed 2009-07-09 nobody gauges 5
2812794 validator problem with reaction ids and L2V1 Closed 2009-06-26 nobody gauges 3
2801571 toXMLString behaves strangely with text nodes Closed 2009-06-05 nobody nobody 5
2799578 flag for conversions from different levels of sbml Closed 2009-06-01 nobody fbergmann 5
2796676 program crashes on windows Open 2009-05-26 nobody nobody 1
2793967 C# bindings build issue with Visual Studio 2003 Closed 2009-05-19 nobody ajourakuProject Admin 5
2793594 problem with documentation of delay AST_nodes Open 2009-05-19 mhuckaSourceForge.net DonorProject Admin s_sahle 5
2787514 'getDerivedUnitDefinition' not const Closed 2009-05-05 nobody luciansmith 5
2787352 Additional RDF not handled Closed 2009-05-05 nobody sarahkeatingProject Admin 5
2783690 Endless cycle if cyclic dependencies in libsbml3.3.1and 2 Closed 2009-04-29 nobody luen 5
2778709 units said not to match, even though they do Closed 2009-04-22 nobody luen 5
2766428 Request: a general getId/getName in libSBML 4 Closed 2009-04-15 nobody luciansmith 5
2763508 Validator gives incorrect line numbers Closed 2009-04-14 nobody luciansmith 5
2749067 Crashing the validator Closed 2009-04-10 nobody luciansmith 5
2748785 leak in AssignmentCycles.cpp Closed 2009-04-09 nobody luciansmith 5
2737310 Model->getSpecies variant with SpeciesReference as object Open 2009-04-06 nobody sarahkeatingProject Admin 3
2737299 addProduct etc using a species Open 2009-04-06 nobody sarahkeatingProject Admin 5
2722083 Severity on VConstraint is misleading Closed 2009-03-30 nobody sarahkeatingProject Admin 5
2716973 C++ doc: missing description Validator constructor Open 2009-03-27 mhuckaSourceForge.net DonorProject Admin alice_villeger 5
2716943 C++ doc: missing description Validator constructor Open 2009-03-27 mhuckaSourceForge.net DonorProject Admin alice_villeger 5
2716938 C++ doc: missing description VConstraint constructor Open 2009-03-27 mhuckaSourceForge.net DonorProject Admin alice_villeger 5
2714870 getSBOTermID crash when no sboterm Closed 2009-03-26 nobody alice_villeger 5
2692696 uninstall/install and upgrading the python bindings Closed 2009-03-18 nobody darrenjw 5
2666458 Copying models out of documents retains stale pointers Open 2009-03-06 sarahkeatingProject Admin luciansmith 5
2657786 v 2.0.2 segfault on WinXP x64 Open 2009-03-03 nobody bheavner 1
2654908 error during docs installation Closed 2009-03-02 mhuckaSourceForge.net DonorProject Admin nobody 5
2648115 Java bindings installation path Closed 2009-02-28 ajourakuProject Admin ajourakuProject Admin 5
2641364 validator misses missing modifier Closed 2009-02-26 nobody luen 5
2641323 validator misses missing modifier Closed 2009-02-26 sarahkeatingProject Admin luen 5
2599679 Python bindings don't work with the latest SWIG 1.3.38. Closed 2009-02-14 ajourakuProject Admin ajourakuProject Admin 5
2543182 problem with UnitDefinition::printUnits() Closed 2009-01-28 nobody s_sahle 5
2515803 Problem with Parameter::getDerivedUnitDefinition() Closed 2009-01-17 nobody s_sahle 5
2498694 documentation typo Closed 2009-01-11 mhuckaSourceForge.net DonorProject Admin s_sahle 5
2478955 An unexpected error has been detected by Java Runtime Enviro Closed 2008-12-31 nobody kmouts 5
2446371 getParentSBMLObject should return derived class Open 2008-12-18 nobody sarahkeatingProject Admin 5
2442566 ModelHistory can have more than one modified date Closed 2008-12-17 sarahkeatingProject Admin sarahkeatingProject Admin 5
2435815 SBMLDocument.checkConsistency() might rely on stale pointers Closed 2008-12-16 sarahkeatingProject Admin lucianoelsmitho 7
2423536 readSBML Closed 2008-12-13 nobody nobody 5
2422813 libSBML can write files with []s in an ID without warning Closed 2008-12-12 sarahkeatingProject Admin lucianoelsmitho 5
2422804 Error reading file with only 'model' tag. Closed 2008-12-12 nobody lucianoelsmitho 5
2422796 Error with input file with only '<sbml>' tag. Closed 2008-12-12 nobody lucianoelsmitho 5
2421989 java bindings broken with gcc 4.3.1 Closed 2008-12-12 nobody troein 5
2418883 segfault with input '<assignmentRule variable="x"/>' Closed 2008-12-12 sarahkeatingProject Admin lucianoelsmitho 5
2418871 Error reading file with '<kineticLaw/>' tag under 'reaction' Closed 2008-12-12 nobody lucianoelsmitho 5
2407173 Build fails on Mac OS X 10.4 Closed 2008-12-08 nobody nobody 5
2376930 Rule 10401 and 10402 not correctly checked by libSBML Closed 2008-12-02 sarahkeatingProject Admin niko-rodrigueProject Admin 3
2219230 Writing out comment doesnt happen Closed 2008-11-03 sarahkeatingProject Admin sarahkeatingProject Admin 5
2209773 compilation errors due to API changes in Xerces 3.0.0 Closed 2008-10-30 ajourakuProject Admin ajourakuProject Admin 5
2209729 crash problem in libSBML built with Xerces on Linux Closed 2008-10-30 ajourakuProject Admin ajourakuProject Admin 5
2189194 crash problem with bzip2 compression Closed 2008-10-23 ajourakuProject Admin ajourakuProject Admin 5
2188734 &amp; is wrongly converted when libXML used Closed 2008-10-23 ajourakuProject Admin ajourakuProject Admin 5
2187684 Units of reaction id used in math expression Closed 2008-10-22 sarahkeatingProject Admin sarahkeatingProject Admin 5
2187675 Checks on a reaction id used in a math expression Closed 2008-10-22 sarahkeatingProject Admin sarahkeatingProject Admin 5
2183855 error codes/categories as strings? Closed 2008-10-21 nobody nobody 5
2183089 Change return type on set/add functions Closed 2008-10-20 sarahkeatingProject Admin sarahkeatingProject Admin 5
2183086 New constructors need documenting Closed 2008-10-20 mhuckaSourceForge.net DonorProject Admin sarahkeatingProject Admin 5
2182856 addCVTerm to object with no metaid Closed 2008-10-20 sarahkeatingProject Admin sarahkeatingProject Admin 5
2175098 dimensionless units having exponents Closed 2008-10-17 sarahkeatingProject Admin nobody 5
2157800 FunctionDefinition using csymbol incorrectly validates Closed 2008-10-10 sarahkeatingProject Admin sarahkeatingProject Admin 5
2146714 syncAnnotation function improved Closed 2008-10-04 nobody sarahkeatingProject Admin 5
2138670 Conversion to L2 marks parameter constant when it shouldnt Closed 2008-09-30 sarahkeatingProject Admin sarahkeatingProject Admin 5
2136796 circular dependency not found during validation Closed 2008-09-29 sarahkeatingProject Admin fbergmann 5
2136530 Adding child to XMLNode does not unsetEnd Closed 2008-09-29 nobody sarahkeatingProject Admin 5
2130568 Inconsistent validation report Closed 2008-09-26 sarahkeatingProject Admin sarahkeatingProject Admin 5
2129044 incorrect writing of function root Closed 2008-09-25 sarahkeatingProject Admin gauges 7
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