generate_homologs : No method for filter for class "list"

[Dalhte]

Hello there I have a problem with the generate_homologs function :

ortholog_resource <- generate_homologs(op_resource = op_resource,

• target_organism = 10116) # Rat [2024-10-19 17:20:23] [SUCCESS] [OmnipathR] NCBI HomoloGene (rescued.omnipathdb.org): downloaded 2 records Erreur dans UseMethod("filter") : pas de méthode pour 'filter' applicable pour un objet de classe "list"

Suspecting a incompatibility problem, I tried to modify the function by forcing dplyr::filtr but to no end Best David

[deeenes]

Hello, This is a networking issue, the "downloaded 2 records" suggests accessing NCBI Homologene failed. The corrupted file in the cache blocks the attempt for a new download, hence it has to be removed. One option is to remove it by hand, based on the log:

library(OmnipathR)

omnipath_set_console_loglevel('trace')
h <- homologene_raw()

# remove corrupted cache content, e.g.
# rm ~/.cache/OmnipathR/17adac3f05a1830fa9196b2637fd2121a4742cbb-1.rds

omnipath_cache_clean_db()

# attempt new download

h <- homologene_raw()

Or wipe the cache completely:

library(OmnipathR)

omnipath_cache_wipe()

If it keeps failing, please share the log (find it by omnipath_logfile()).

[Dalhte]

Thx a lot ! it's working :)))

Best David