libsbml

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## Description This change adds prinf style formatting to Rf_error calls. Without this, compilation fails when -Wformat-security is passed to gcc. ``` /home/spot/git/libsbml/libsbml-5.20.2/build/src/bindings/r/libsbml_wrap.cpp:330601:17: error: format not a string literal and...

spotaws

Hi all, The `AssignmentCycles::determineAllDependencies()` function does not behave well with models having many parameters and rules and transitive dependencies between model constructs. Unfortunately, I cannot share any of the actual...

eltix

Typo in the tag name

1

I found a typo during *syntactic* testing in the file `syntactic_tests.v3.4.0/syntactic/21104/21104-fail-01-13-sev2-l3v1.xml` on line 33 where element name is `modiferSpeciesReference` (missing 'i', correct modifierSpeciesReference).

SolunarNexus

The original version of these files was indeed wrong as per the failure they are supposed to test, but it's slightly more likely that someone might make a mistake putting...

luciansmith

Unit validation with distrib uniform not working

4

Hi all, I have an SBML model with an initial assignment from a uniform distribution (model attached). [spt_random.zip](https://github.com/sbmlteam/libsbml/files/14117972/spt_random.zip) Despite having set the units on the distributions I get a unit...

matthiaskoenig

## Description The CMake configuration does not respect the user option "-DBUILD_SHARED_LIB=". Package managers (and users) commonly use this main configuration option to decide whether to build the project as...

Waschina

File 99107-fail-01-06-10102 not actually wrong

1

We test for error 99107 in the file 99107-fail-01-06-10102.xml, but the problem it detects is, I believe, not actually an error. The file defines a new namespace 'appear' and adds...

luciansmith

Can't install SBML in MATLAB 2023b

1

I need libsbml to use GenSSI [GenSSI](https://github.com/genssi-developer/GenSSI), but I cannot install SBML in MATLAB. I am fllowing the instructions in [this documentation](https://sbml.org/software/libsbml/libsbml-docs/installation/), but I cannot use SBML in either case:...

Elisshaze

Add piecewise-to-events translators

1

We found a model that didn't work correctly on roadrunner, since there was a piecewise equation that only changed for a window of time that wasn't checked by the CVODE...

luciansmith

FBC: Can't make package version 3 object in L3v2 core model.

1

It's impossible to create a flux objective and add it to an L3v2 model: * If you run createFluxObjective(), it gives you an object with a getLevel() of 3, a...

luciansmith