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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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get_collectri broken from omnipathdb.org website being down #144

Closed omsai closed 4 hours ago

omsai commented 5 hours ago

decoupleR::get_collectri() relies on the https://omnipathdb.org which is down.

BiocManager::install(c("decoupleR", "OmnipathR"))

library(decoupleR)

tftg <-
   get_collectri(organism = "human",
                 split_complexes = FALSE)
[2024-11-14 15:01:00] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` (attempt 1/3); error: cannot open the connection
[2024-11-14 15:01:07] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` (attempt 2/3); error: cannot open the connection
[2024-11-14 15:01:12] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` (attempt 3/3); error: cannot open the connection
[2024-11-14 15:01:12] [WARN]    [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`; error: cannot open the connection
[2024-11-14 15:01:12] [WARN]    [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
Error in if (.keep) . else select(., -!!evs_col) : 
  argument is of length zero
In addition: Warning messages:
1: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic': The requested URL returned error: 500 
2: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic': The requested URL returned error: 500 
3: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic': The requested URL returned error: 500

Screenshot From 2024-11-14 15-09-44

deeenes commented 4 hours ago

It's up and running again. Thanks for reporting, and apologies for the inconvenience!