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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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Error in mutate() when running get_dorothea() #69

Closed dano602 closed 1 year ago

dano602 commented 1 year ago

Hello everyone. I have encountered an issue when trying to run get_dorothea function from decoupleR according to this tutorial: https://saezlab.github.io/decoupleR/articles/tf_bk.html When I run net <- get_dorothea(organism='human', levels=c('A', 'B', 'C')) I get this error: Error in mutate(): ℹ In argument: n_references = ifelse(...). Caused by error in map(): ℹ In index: 1. Caused by error in .f(): ! Arguments in ... must be passed by position, not name. ✖ Problematic argument: • outsep = outsep When I tried to run get_dorothea for the first time, it mentioned missing some packages that I installed and after that, I got stuck with this error message. I tried to install version of decoupleR from both Bioconductor and GitHub, I tried to reinstall dplyr and also installed dorothea from github. However, nothing sorted my issue. I tried get_progeny() and it works just fine. I browsed in opened issues but did not see someone facing similar problem, but maybe I missed it. I am relatively new to R so there may be something that I am missing. I appreciate your help.

deeenes commented 1 year ago

This was an issue in OmnipathR that developed due to api changes in the latest updates of purrr and rlang. Should be fixed now on master: https://github.com/saezlab/OmnipathR/issues/57

dano602 commented 1 year ago

Reinstalling OmnipathR from GitHub solved my issue. Thank you very much for your help. :)