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MetaSys-LISBP / IsoSim

IsoSim: stoichiometric, kinetic and isotopic modeling of metabolic systems
https://www.biorxiv.org/content/10.1101/735308v1
GNU General Public License v3.0
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isosim_test() showing error #1

Open CarolinaCorona opened 1 year ago

CarolinaCorona commented 1 year ago

Error in isosim_test()

Downloaded the zip file from GitHub page (https://github.com/MetaSys-LISBP/IsoSim)

Unzipped the file and changed working directory for easier access to the R scripts

setwd("C:/.../IsoSim-2.0.0/isosim/") source("nlsic.R") source("isosim.R")

Running isosim_test() showed the following error after "...calculate fluxes...":

Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: the condition has length > 1

When running the isosim_test() line by line (after setin the working directory to original) and changing the numCores & mc.cores to NULL I do get more lines but it gets stuck at:

calculate fluxes for all subsystems

res_sub <- fit_subsystems(subsystems, dirname="fit_minimal_subsystems", mc.cores=numCores)

And the error is:

Error in if (class(a) != "qr") { : the condition has length > 1

Any idea how can I get it to work? I have RTools43 and R version 4.3.1 (2023-06-16 ucrt)

pierremillard commented 1 year ago

Dear @CarolinaCorona ,

thanks for your message. Before trying to solve the error, could you let me know for which usage you want to use IsoSim?

If this is related to our work on ScalaFlux, just to let you know that the proposed approach has been implemented by @sgsokol in influx_si (software at https://github.com/sgsokol/influx ; doc at https://influx-si.readthedocs.io ). I use IsoSim mainly for development purposes, to test new approaches, but it has not been designed for users to be stable in a production environment (more as a poc). In contrast, influx is a more robust tool and should be used preferentially.

I'll try to fix the error anyway, I'll come back to you to get additional details.

Best, Pierre

CarolinaCorona commented 1 year ago

Hello Mr. Millard,

Sorry for the late reply. I am interested in using the package for the construction of the model and the simulation of the metabolism of cyanobacteria under dynamic conditions. I am currently trying to take one of the models provided to understand the construction of the network. Thank you for your help and if other information is needed, let me know.

Kind regards,

Carolina Corona

On Wed, 26 Jul 2023 05:09:09 -0700 Pierre Millard @.***> wrote:

Dear @CarolinaCorona ,

thanks for your message. Before trying to solve the error, could you let me know for which usage you want to use IsoSim?

If this is related to our work on ScalaFlux, just to let you know that the proposed approach has been implemented by @sgsokol in influx_si (software at https://github.com/sgsokol/influx ; doc at https://influx-si.readthedocs.io ). I use IsoSim mainly for development purposes, to test new approaches, but it has not been designed for users to be stable in a production environment (more as a poc). In contrast, influx is a more robust tool and should be used preferentially.

I'll try to fix the error anyway, I'll come back to you to get additional details.

Best, Pierre

-- Reply to this email directly or view it on GitHub: https://github.com/MetaSys-LISBP/IsoSim/issues/1#issuecomment-1651680020 You are receiving this because you were mentioned.

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