I received a warning message when loading the CollecTRI network. The function still executes as expected, but I wanted to report it in case it affects future compatibility.
> packageVersion("decoupleR")
[1] ‘2.14.0’
> packageVersion("OmnipathR")
[1] ‘3.16.0’
> net = decoupleR::get_collectri(organism = 'human',
+ split_complexes = FALSE)
[2025-06-06 08:54:42] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-06-06 08:54:43] [SUCCESS] [OmnipathR] Loaded 232 interactions from cache.
Warning messages:
1: In OmnipathR::import_tf_mirna_interactions(genesymbols = TRUE, resources = "CollecTRI", :
'OmnipathR::import_tf_mirna_interactions' is deprecated.
Use 'tf_mirna' instead.
See help("Deprecated")
2: In readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
I received a warning message when loading the CollecTRI network. The function still executes as expected, but I wanted to report it in case it affects future compatibility.