Error connecting to external databases through celldex
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swbarnes2 ▴ 890
@swbarnes2-14086
Last seen 19 minutes ago
San Diego

My organization's IT policies have tightened up with regard to making external connections, and I'm getting errors like

localHub=TRUE
library(celldex)
mouse_imm_ref <- celldex::ImmGenData()

Error in value[[3L]](cond) : failed to connect
  reason: SSL certificate problem: unable to get local issuer certificate
  Consider rerunning with 'localHub=TRUE'

I think the issue is that there is some kind of list of allowed locations, and I need to ask IT to add the locations that celldex queries to that list. But looking at the function definitions is not helping me to know what exactly I need to request of IT. Can you help me to know where to look for the data locations, so I can ask IT to allow connections there? Is it maybe just github or git.bioconductor.org?

celldex • 94 views
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Mike Smith ★ 5.2k
@mike-smith
Last seen 4 minutes ago
EMBL Heidelberg / de.NBI

I've seen this error with Ubuntu 20.04 and the Ensembl mirror sites, where there's some oddity in the SSL certificates. It comes up often enough I put it in the vignette

Can't promise this will work with Celldex (or that it's a good idea), but maybe try running this:

httr::set_config(httr::config(ssl_verifypeer = FALSE))

If that doesn't work, I think the server it's connecting to is https://experimenthub.bioconductor.org

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That line of code works. I don't think that's the right location for the data, because I can get to it by browser, so my org has not locked down access.

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