#481 libsbml installation in R via R-GUI

[Elif Emanetci]

Hello,

I download libSBML zip file and I tried to install this package in R via R GUI but I got an error:
"package or namespace load failed for ‘libSBML’:
package ‘libSBML’ was installed before R 4.0.0: please re-install it"
I deleted libSBML file from the document and reinstall that packge but I got same error. Can you help me?

Elif

[Frank Bergmann]

If you tell me what operating system you use and whether 32 or 64 bit R interpreter, i can create some bindings for you. Sorry, we have not gotten around to making a new release for the newer R versions.

[Elif Emanetci]

64 bit. I have just seen that libSBML was created for R 3.3.3 or older versions. I am using 4.0.
thank you.

[Frank Bergmann]

Here a version of libSBML for R 4.0.2 (win x64):

https://share.getcloudapp.com/mXu6DkoX

[Elif Emanetci]

hello again,
I have updated my R version from 4.0.2 to 4.0.3 and the zip file you sent me last week did not work properly. Do you have R4.0.3 version of LibSBML? And can I have it?

[Frank Bergmann]

can you please provide an error message, as to what went wrong?

[Elif Emanetci]

installing zip file is okey but when I try to read xml file (which was readed properly in my previous R version) this message occurs:

Warning messages:
1: In readSBMLmod("iBrain_210420.xml", bndCond = FALSE) :
Missing FBC-plugin for libSBML. FBC constraints will be ignored.
2: In readSBMLmod("iBrain_210420.xml", bndCond = FALSE) :
Missing Groups-plugin for libSBML. Groups will be ignored.

It affects my analysis because file is not readed properly.

thank you.

[Frank Bergmann]

I think we have to first find out, what is going on here. As the binaries ive created do support the SBML Level 3 FBC and Groups Extensions. Is there a way i can reproduce what happened on your machine locally?

if i just recompiled, i don't expect any changes for R 4.0.2 and 4.0.3, that would explain what is going on here.

[Elif Emanetci]

you can run this code in R4.0.3, it creates same warning message:

install.packages("sybilSBML")
library(sybilSBML)
dir <- system.file(package = "sybilSBML", "extdata")
file <- file.path(dir, "ecoli_core_model.xml")
mod <- readSBMLmod(file, bndCond = FALSE)

also, there is no function in help page of the libSBML package in R4.0.3.

[Frank Bergmann]

That would explain it. Here is what is happening. The sybilSBML package, does not use the libSBML R bindings at all. Instead it includes a precompiled libSBML (version 5.8.0 on windows) and exposes a subset of the functions there. So there is not much we can help you out there, and you would have to contact them to figure out how to get a newer libSBML version that works with sybil.

[Elif Emanetci]

Okey,
Thank you for your help and interest.

[Elif Emanetci]

thank you very much.