Sybil Error: needs an object of class modelorg, Matrix or matrix!

[NatashaJorge]

Hello,

I'm having problems trying to use the BacArena package.

I am in a conda environment and, with the exception of BacArena itself, I've installed all requirements with conda (glpkapi, sybil, devtools, rsbml, libsbml).

I've tried running the following lines:

library("BacArena")
library("rsbml")
test = rsbml_read("GCF_014131675.pFBA.xml", dom=F)
bac = Bac(test)
Error in sybil::findExchReact(model) :
needs an object of class modelorg, Matrix or matrix!
q()

I've seen the Issue on #116 suggesting the manual installation of sybilSBML. The R command itself (R CMD INSTALL sybilSBML_3.1.3.tar.gz) cannot link with the libsbml library and ask for its path:

configure: error: Could not link to libSBML:
use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.
ERROR: configuration failed for package ‘sybilSBML’

Once you give the libSBML path, it looks for a readSBML library which does not exist in the libsbml path:

checking for library containing readSBML... no
configure: error: Could not link to libSBML:
use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.

I've also trying to install libSBML without conda (with the R CMD INSTALL libSBML_5.19.0.tar.gz command), but there is no readSBML there either.

Please, do you know a way to either: read the sbml file as a matrix compatible with sybil or install a libsbml with the readSBML for sybil?

Thanks for the time and attention,
Best,
Natasha

[maringos]

Hi,

You need the R package sybilSBML for reading SBML models (see function readSBMLmod).

In Ubuntu it is enough to follow the instructions given here. Have you tried that approach?

Do you have another OS? Please read here.

Best,
Yorgos