Error while running COSMOS tutorial in R

[dilipgosar]

Dear Sir/ Madam,

I am trying to run tutorial mentioned on COMSOS website but it is giving me this error.

test_result_back <- format_COSMOS_res(test_result_back,

•                                   metab_mapping = metabolite_to_pubchem,
  

•                                   measured_nodes = unique(c(names(toy_metabolic_input),
  

•                                                             names(toy_signaling_input))),
  

•                                   omnipath_ptm = omnipath_ptm)
  

Error in as.data.frame(cosmos_res$weightedSIF) :
object 'test_result_back' not found

I am running the R code exactly mentioned in the tutorial and I like to know if you can fix it. Also I like to know if you can provide more examples of how to use COSMOS.

Appreciate your help.

Sincerely,

Dilip Gosar

[Attila Gabor]

Dear Dilip Gosar,

sorry, the tutorial is a bit outdated. Please, follow the package vignette instead.
I will try to synchronize them today, so hopefully in a few hours, they will be identical.
best,
Attila

[Attila Gabor]

tutorial is now updated.
the github page will be updated in 4-5 mins.

[dilipgosar]

Hello Attila,

Thank you for your reply. I was trying to find the cosmosR package vignette but could not find it. It is giving me one more error. I have loaded the cosmosR library in R. Then I was running the following code

CARNIVAL_options <- default_CARNIVAL_options(solver = "lpSolve")
Error in default_CARNIVAL_options(solver = "lpSolve") :
unused argument (solver = "lpSolve")

I don't know what this error means. I like to know how you can help me.

Appreciate your help.

Sincerely,

Dilip Gosar

[Attila Gabor]

Hi,
that means you are not using the latest version, please update to cosmos v1.3, at least.

You can install from our github

remotes::install_github("saezlab/cosmosR")

or
from Bioconductor,

BiocManager::install("cosmosR")

in this case make sure that your BiocManager is up to date (the current release is 3.15).

best
Attila