[Bioc-devel] SSL error on Ubuntu 20.04

[Mike Smith]

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> 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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