[Bioc-devel] nebbiolo SSL-related build error

[Karl Stamm]

Yes, thank you so much.
I think the most reliable solution is to remove the biomart calls from
my package processes.
I can use the AnnotationDbi for the same purposes and hardly have any
difference in outcome.


On Thu, Mar 31, 2022 at 3:08 AM Hervé Pagès <hpages.on.github using gmail.com> wrote:
>
> Hi Karl,
>
> Unfortunately this Ensembl SSL certificate problem is not specific to
> our Linux builder nebbiolo1 but it affects Ubuntu users in general. I
> can reproduce it on my laptop (Ubuntu 21.10):
>
>      library(biomaRt)
>      mart <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL",
> host="https://www.ensembl.org")
>      # Ensembl site unresponsive, trying asia mirror
>      # Error in curl::curl_fetch_memory(url, handle = handle) :
>      #   SSL certificate problem: unable to get local issuer certificate
>
> and on our Docker image (Ubuntu 20.04):
>
>      library(biomaRt)
>      mart <-  biomaRt::useMart("ENSEMBL_MART_ENSEMBL",
> host="https://www.ensembl.org")
>      # Ensembl site unresponsive, trying uswest mirror
>      # Error in curl::curl_fetch_memory(url, handle = handle) :
>      #   server certificate verification failed. CAfile: none CRLfile: none
>
> For some reason the error is not exactly the same on the two systems.
> Also note that the error is intermittent: sometimes the call to
> biomaRt::useMart() succeeds and sometimes it doesn't, so you might need
> to call biomaRt::useMart() several times before you actually get the error.
>
> Here is my understanding of this situation and how it can be mitigated
> (others on this list more familiar with this issue please correct me if
> I'm wrong):
>
>    - This issue has been around for a while and discussed in various places.
>
>    - IIRC the problem really is on Ensembl's side but we only see the
> biomaRt::useMart() error on Ubuntu >= 20.04 because this OS has
> increased security settings by default.
>
>    - I also believe that the Ensembl folks have been aware of the
> situation for a while but AFAICT not much has changed.
>
>    - IIRC a workaround is to lower the security settings on the system.
> However this is not a totally satisfying solution because Ubuntu users
> wouldn't necessarily know how to do that or have the permission to do it
> (e.g. if they are on a cluster).
>
>    - In January Mike Smith modified biomaRt::useEnsembl() so that the
> function should be able to use its own SSL settings to better handle the
> SSL certificate situation on Ubuntu. So using biomaRt::useEnsembl()
> instead of biomaRt::useMart() should help.
>
>    - Regardless of Mike's recent improvement to biomaRt::useEnsembl(),
> it's probably a good idea to use this function instead of
> biomaRt::useMart() when accessing the Ensembl Mart.
>
>    - The sad reality is that Ensembl Mart has always been a flaky
> service. So no matter how we access it, we sometimes get errors like
> this one:
>
>      mart <- useEnsembl("genes")
>      # Ensembl site unresponsive, trying asia mirror
>      # Error: Unexpected format to the list of available marts.
>      # Please check the following URL manually, and try ?listMarts for
> advice.
>      #
> https://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt
>
> Hope this helps,
>
> H.
>
> On 30/03/2022 13:11, Karl Stamm wrote:
> > I have a new build error that is somewhat environment specific;
> > failing only on nebbiolo and not for Windows nor Mac.
> >
> > The error message states only " SSL certificate problem: unable to get
> > local issuer certificate "
> >
> > My package, during a rather long process, includes a call to biomart with
> > biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="https://www.ensembl.org")
> >
> > In a previous version I did not specify "https" but simply 'www', and
> > we did not have any build errors, but Ensembl was throwing warnings
> > (recently?) that an https specification will become mandatory.
> > I guess nebbiolo has some SSL inability, which puts me in a bind, to
> > either use a deprecated interface and hope Ensembl keeps working, or
> > seek whatever problem we're having during the builds.
> >
> > Thanks for your insight.
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>