cannot open the connection to 'https://omnipathdb.org/resources'

[jtorrejon81]

Hello,

Many thanks for the nice tool. I was using OmnipathR without any problem during all year but Today when I tried to load the prior knowledge interactions, composed by kinase-target relationships

uniprot_kinases <- OmnipathR::import_omnipath_annotations(resources = "UniProt_keyword") %>%
dplyr::filter(value == "Kinase" & !grepl("COMPLEX", uniprot)) %>%
distinct() %>%
pull(genesymbol) %>%
unique()

I got the following error related to connection problem to Omnipath server

Error in file(con, "r") :
cannot open the connection to 'https://omnipathdb.org/resources'

I am wondering if it is due to a server issue since there was a very similar issue (#92) two days ago

Many thanks for your help
Best,
Jacob

[deeenes]

Hello Jacob,

Thanks for reporting this issue. The reason this time was insufficient resources (especially memory) in the server. As a quick fix I manually restarted the service now, though this error might pop up again, until hopefully in 1-2 months from now we address the real performance issue.

Best,

Denes

[jtorrejon81]

Many thanks Denes for your quick reply and help

Best,
Jacob