Error in do.call(stop, list(m), envir = env)

[Megan0921]

Dear Team, I'm trying to use decoupleR to retrieve CollecTRI from OmniPath and have encountered an error when running the command "collecTRI <- decoupleR::get_collectri(organism='human', split_complexes=FALSE)":

collecTRI <- decoupleR::get_collectri(organism='human', split_complexes=FALSE)
#> [1] TRUE
#> Error in do.call(stop, list(m), envir = env): `only_from` can be called only on data frames with `evidences` column.

^{Created on 2024-07-13 with reprex v2.1.1}

The error occurred when I’m following the tutorial on "Transcription factor activity inference in bulk RNA-seq". I am using OmnipathR version 3.13.5 and decoupleR 2.9.7.

How can I fix this problem? Look forward to your reply. Thanks a lot!

[deeenes]

Hi @Megan0921, Since apparently the issue was an old cache item, I recommend you to wipe your cache, so the error never happens again. To do so, run in a new R session:

library(OmnipathR)
omnipath_cache_wipe()

[Megan0921]

Yes, that worked. Thanks a lot!@deeenes