[Bioc-devel] SSL error on Ubuntu 20.04

[Selles Vidal, Lara]

Hi Mike,

Thanks a lot, I was able to fix all errors using a similar approach

Best wishes,

Lara

On 1 Oct 2020, at 11:10, Mike Smith <grimbough using gmail.com<mailto:grimbough using gmail.com>> wrote:

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Hi Lara,

I've encountered this issue with biomaRt too.

I found I could get the connection to work with the following:

library(httr)
url <- "https://www.ensembl.org/"
httr_config <-  config(ssl_cipher_list = "DEFAULT using SECLEVEL=1")
res <- with_config(config = httr_config, GET(url))

I haven't quite decided the best way to integrate that into my package, for now it uses the httr_config if it's running on any Linux, which seems quite heavy handed. It may be that specifying a particular cipher or determining the host capabilities would be preferable to "DEFAULT", but does seem to work for now on Ubuntu 20.04 and hasn't thrown any problems for my tests on 16.04 and 18.04.

Best,
Mike

On Wed, 30 Sep 2020 at 21:02, Selles Vidal, Lara <lara.selles12 using imperial.ac.uk<mailto:lara.selles12 using imperial.ac.uk>> wrote:
Dear BioC community,

We were recently informed that a multilayered bug due to an increased security level in Ubuntu 20.04, configuration issues on server side and a bug in OpenSSL 1.1.1 caused our packages to fail on Ubuntu 20.04 with the following error:

   error:14094410:SSL routines:ssl3_read_bytes:sslv3 alert handshake failure

This affects the two packages I maintain, rfaRm and ncRNAtools. As a temporary fix, we were suggested to use HTTP instead of HTTPS. However, some of the web resources accessed with our packages do not seem to be accessible via HTTP. This is reflected in the latest build for rfaRm for example (http://bioconductor.org/checkResults/devel/bioc-LATEST/rfaRm/) , which fails as a consequence of all the URLs being changed to the “http” version instead of “https”.

The problem seems to have been discussed here https://github.com/Ensembl/ensembl-rest/issues/427 , with a temporary fix suggested here https://askubuntu.com/questions/1233186/ubuntu-20-04-how-to-set-lower-ssl-security-level . However, this seems to involve changing some openssl options through the openssl config file. We are unsure on whether this temporary fix could be implemented from within our package. We would greatly appreciate any guidance on how to implement it, or on any other alternative temporary workarounds.

Thanks a lot in advance!

Best wishes,

Lara

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