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Bioconductor / KEGGREST

Client-side REST access to KEGG
https://bioconductor.org/packages/KEGGREST
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OpenSSL error when using keggLink #20

Open GMFranceschini opened 1 year ago

GMFranceschini commented 1 year ago

Hello, thank you for developing the package. Currently, I have a connection problem using this code:

library(KEGGREST)
library(org.Hs.eg.db)
library(tidyverse)

# get pathways and their entrez gene ids
hsa_path_entrez  <- keggLink("pathway", "hsa") %>%
    tibble(pathway = ., eg = sub("hsa:", "", names(.)))
Error in curl::curl_fetch_memory(url, handle = handle) : 
  OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0

Ubuntu 22.04, R 4.2.1

Could you please advise?

hpages commented 1 year ago

Does curl https://rest.kegg.jp/link/pathway/hsa work in a terminal?

You could also try:

library(curl)
res <- curl::curl_fetch_memory("https://rest.kegg.jp/link/pathway/hsa")

If the above fails then it's not a KEGGREST issue per se.

Some googling around seems to indicate that this is an issue with OpenSSL on Ubuntu 22.04. Someone asked about this on SO and the top answer suggests to update all packages on the machine with sudo apt update && sudo apt upgrade -y. A reboot might be needed on completion I don't know.