[Bioc-devel] pandoc SSL error on malbec2 and tokay2

[Nan Xiao]

Hey Martin,

- thanks a lot for the very detailed reply. I appreciate the great
efforts your team has made, and I understand that it's hard to keep
everything in check especially on a large scale. :)

I dug further into the issue, and eventually, it seems to be a problem
in the communication between hs-tls and Google servers:
https://github.com/vincenthz/hs-tls/issues/152 . So my temporary fix was
switching to a third-party reverse proxy of the Google Fonts service.
Indeed, further transient Internet issues may sometimes happen when the
connection is bad, so migrating back to BiocStyle sounds like a good
long-term solution.

Thanks again,
-Nan

-- 
https://nanx.me

On Wed, Sep 6, 2017, at 14:48, Martin Morgan wrote:
> On 09/05/2017 10:35 AM, Nan Xiao wrote:
> > Hey Kasper,
> > 
> > - I really appreciate your help. Although it didn't help answer the
> >    question directly, I think it would still be necessary to clarify
> >    some facts:
> > 1. I agree that using "non-standard fonts" could bring better aesthetics
> >     for a particular group of people -- maybe not everyone. But the
> >     "occasional" build problem should not be a reason why this
> >     personalization is discouraged. In fact, such build problem should
> >     not happen a lot (or, at all). I have been using such non-standard
> >     fonts for my 9 regularly updated R packages on CRAN since 2015, and I
> >     didn't encounter a single vignette build issue.
> > 2. I've used BioCStyle since 2014, but eventually decided to switch to
> >     my own style years later because of the frequent build errors it
> >     caused back then. Maybe that's only my personal, limited experience
> >     (and I've seen the recent BioCStyle v2 got a lot of improvements),
> >     but this is the main reason why I trust the document style
> >     controllable by myself more than the other options.
> 
> It's great that CRAN is so efficient and robust; I really don't know how 
> they do it.
> 
> I'll re-iterate with Kasper that these customizations cost us 
> (Bioconductor core team) time -- maybe your package fails only once 
> every 1000 days, but there are a thousand developers so...
> 
> Fixing BiocStyle once fixes it for all developers, while fixing a custom 
> issue once fixes it for just one developer.
> 
> And users can choose to build vignettes, so they'll have to 
> trouble-shoot whatever issues are unique to your package.
> 
> There really is value all around in keeping things simple.
> 
> As for your particular issue, it seemed to fail on 3 of the 5 builds 
> that have reported yesterday, 2 of the five today. Have you noticed this 
> for several days in a row?
> 
> I did ask about pandoc on the builders; they have
> 
>    malbec1/2 are at version 1.19.1
>    tokay1/2 have 1.17.2
>    veracruz1/2 have 1.19.2.
> 
> of course we try to keep these in sync, but also do not go to 
> extraordinary lengths to install the same version across platforms. 
> These have not changed in the time frame that would cause your builds to 
> experience recent failures.
> 
> This seems very much like a transient Internet access issue. Transient 
> access is one of the most difficult to debug, especially on our 'build' 
> servers where the loads experienced by the machines can vary a lot, and 
> where the vagaries of Internet connections can be catastrophic for a 
> build but almost unobserved by an individual investigating the problem.
> 
> Martin
> 
> > Best,
> > -Nan
> > 
> > --
> > https://nanx.me
> > 
> > 
> > On Tue, Sep 5, 2017, at 09:16, Kasper Daniel Hansen wrote:
> >> Build errors like these (related to processing of vignettes) happens
> >> occasionally.  I _strongly_ suggests not not using non-standard fonts
> >> or advanced layout features.  The small advantage of this (better
> >> aesthetics according to the package writer, but not always according
> >> to everyone who reads it) does not outweigh the disadvantage of
> >> package failure and associated time burden on the package authors and
> >> the build system / admins.  I strongly suggests using BiocStyle; I
> >> know that the layout doesn't agree with everyone, but (1) you can
> >> expect that the build system will support this and (2) aesthetics is
> >> highly personal anyway.>
> >> Best,
> >> Kasper
> >>
> >> On Mon, Sep 4, 2017 at 12:38 PM, Nan Xiao <me at nanx.me> wrote:
> >>> Dear BioC,
> >>>
> >>>   - I see some very recent build errors for my packages (vignettes)
> >>>     which>>  use Google Fonts:
> >>>
> >>>   pandoc: Could not fetch
> >>> https://fonts.googleapis.com/css?family=Alegreya+Sans:400,400i,700
> >>>   TlsExceptionHostPort (HandshakeFailed Error_EOF)
> >>>   "fonts.googleapis.com">>  443
> >>>
> >>>   For example
> >>> https://bioconductor.org/checkResults/release/bioc-LATEST/Rcpi/malbec2-buildsrc.html>>
> >>>   There were no such issues building these vignettes before, and
> >>>   I'm not>>  even sure if this is a new issue caused by Google or pandoc.
> >>>   Could you>>  please shine some light on this?
> >>>
> >>>   Thank you,
> >>>   -Nan
> >>>
> >>>   --
> >>> https://nanx.me
> >>>
> >>>   _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> > 	[[alternative HTML version deleted]]
> > 
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
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