"R-package sybilSBML not found. Please install sybilSBML for sbml output."

[stonescoding]

Good day,

I have installed gapseq using the following command:

mamba create -c conda-forge -c bioconda -n gapseq gapseq

The installation is successful, and the gapseq function works. The problem however is that the gapseq fill function does not generate xml files. I am interested in having xml files as those serve as input for the r library cobrar. The warning message I receive when the gapseq fill function terminates is the following:

"R-package sybilSBML not found. Please install sybilSBML for sbml output."

Is there someone that can help me with this issue? Thanks.

[Waschina]

Hi @stonescoding ,

The problem is that the gapseq version on bioconda is not the latest development version of gapseq and it still relies on sybil and sybilSBML.

There are two possible solutions at the moment:

1. Try to install the R-package sybilSBML within your conda environment called "gapseq." This can be tricky in some cases, as sybilSBML does not work with the latest libSBML versions.
2. Try to install the development version of gapseq (without conda).

We are also planning to make a new gapseq release in the following few days, which hopefully will get picked up by Conda soon after. Then, also the bioconda installation should, in principle, work.