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: error in `str_to_upper()` OmnipathR #105

Closed maartenciers closed 10 months ago

maartenciers commented 10 months ago

Hey, I'm currently trying to use decoupleR using the vignette (https://saezlab.github.io/decoupleR/articles/tf_sc.html) but I'm unable to run get_collectri function, due to a problem loading the OmnipathR package I tried reinstalling decoupleR, OmnipathR and even the stringi package multiple times but the problem persists. Can you help me resolve this issue?

library(decoupleR) 
net = get_collectri(organism='human', split_complexes=FALSE)

Error: package or namespace load failed for ‘OmnipathR’:
 .onLoad failed in loadNamespace() for 'OmnipathR', details:
  call: map2(., names(.), function(val, key) {
  error: ℹ In index: 1.
ℹ With name: omnipath.url.
Caused by error in `str_to_upper()`:
! lazy-load database '/home/maartenc/R/x86_64-redhat-linux-gnu-library/4.3/stringi/R/stringi.rdb' is corrupt
In addition: Warning messages:
1: In str_to_upper(.) : restarting interrupted promise evaluation
2: In str_to_upper(.) : internal error -3 in R_decompress1

> packageVersion('decoupleR')
[1] ‘2.9.1’
> packageVersion('OmnipathR')
[1] ‘3.11.1’
> packageVersion('stringi')
[1] ‘1.8.2’
deeenes commented 10 months ago

Typically this issue is solved by restarting the R session. Please let me know if it doesn't.

maartenciers commented 10 months ago

Indeed! Thx