Switching to Gurobi solver for running COSMOS

[SwagatikaSahoo2023]

Dear Saez Lab
Thanks for your support earlier.
I have setup COSMOS in R, and currently running into issues while using the Gurobi solver.
Below is a copy of the console.

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Loading required package: slam
[1] "Adding compartment codes."
Error in match.arg(solver, choices = solver_options) :
'arg' should be one of “lpSolve”, “cplex”, “cbc”

source("~/MOMI_Project/Vantage_OMICsAnalysis/to_SS_for_cosmos/run_cosmos_nbc_recent.R")
[1] "Adding compartment codes."
Automatic setup path for cplex solver is not support for Windows yet.
[1] "COSMOS: 145 input/measured nodes are not in PKN any more: Metab__HMDB0003454_c, Metab__HMDB0014828_c, Metab__HMDB0035589_c, Metab__HMDB0061683_c, Metab__HMDB0040865_c, Metab__HMDB0041272_c and 139 more."
[1] "COSMOS: 183 input/measured nodes are not in PKN any more: ZNF723P, AC008984.2, VDAC1P4, PEX5L, RP11-252I13.1, RFPL1 and 177 more."
[1] "COSMOS: all 4 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 23 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 6 of the 15 genes in expression data were found as transcription factor target"
[1] "COSMOS: 6 of the 5321 transcription factor targets were found in expression data"
[1] "COSMOS: removing nodes that are not reachable from inputs within 5 steps"
[1] "COSMOS: 59839 from 83556 interactions are removed from the PKN"
[1] "COSMOS: 20 input/measured nodes are not in PKN any more: Metab__HMDB0001930_c, Metab__HMDB0014389_c, Metab__HMDB0014633_c, Metab__HMDB0014928_c, Metab__HMDB0003791_c, Metab__HMDB0000228_c and 14 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 5 steps"
[1] "COSMOS: 21226 from 23717 interactions are removed from the PKN"
[1] "COSMOS: 2 input/measured nodes are not in PKN any more: FOXA1, HNF4A and 0 more."
[1] "COSMOS: 133 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
--- Start of the CARNIVAL pipeline ---
16:12:53 05.06.2023 Carnival flavour: vanilla
16:12:53 05.06.2023 Generating variables for lp problem
16:12:53 05.06.2023 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: C:/Users/vanta/OneDrive/Documents/MOMI_Project/Vantage_OMICsAnalysis/to_SS_for_cosmos/parsedData_t16_12_53d05_06_2023n43.RData
16:12:53 05.06.2023 Generating formulation for LP problem
16:12:53 05.06.2023 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: C:/Users/vanta/OneDrive/Documents/MOMI_Project/Vantage_OMICsAnalysis/to_SS_for_cosmos/lpFile_t16_12_53d05_06_2023n43.lp
16:12:54 05.06.2023 Solving LP problem
Writing cplex command file
Done: writing cplex command file
Saving results...
Error in solversFunctions$solve(carnivalOptions) :
CPLEX solution file is not found. CPLEX was likely interrupted (exceeding memory limit is the usual cause).
Try to increase the available resources (memory) or reducing the PKN.
In addition: Warning message:
In file.remove("cplex.exe") :
cannot remove file 'cplex.exe', reason 'No such file or directory'

Please advise further.
Please note that I am using Gurobi, but due to default_CARNIVAL_options, I have written it as "cplex".
Best
Swagatika Sahoo