Compilation fails with libsbml>=5.19

[cdiener]

Describe the bug

sybil-SBML will raise compilation errors during install with libSBML version 5.19 or above.

Steps to reproduce

Install a recent libSBML, then run

remotes::install_github("SysBioChalmers/sybil-SBML")

Expected behavior

Package should install without errors.

Logs

A full build log is here

[Waschina]

Hi @cdiener

I am not a maintainer of sybilSBML, but from the log file, it seems like the issue causes problems in your gapseq docker. We (the gapseq developers) are aware of the issues associated with the Sybil-family packages. We are currently working on a slim R package that includes SBML support and basic COBRA methods. The new package will replace the sybil dependencies in one of the next gapseq versions.

In the meantime, you could turn off SBML output in the gapseq workflows and translate the output models (in RDS format) to SBML using the development version of cobrar.

# remotes::install_github("Waschina/cobrar")
library(cobrar)

mod <- readSybilmod("<model.RDS>")
writeSBMLmod(mod, file_path = "<model.xml>")

[cdiener]

Thanks Silvio. I pinned libsbml to an older version in the docker so for now it's working there. But good to hear you're developing a new interface. Best of luck.