[Bioc-devel] macOS auto build fails with "graphics API version mismatch"

[Hervé Pagès]

Hi Matteo,

Let's please keep this conversation on bioc-devel where it started.

On 23/03/2022 08:46, Matteo Tiberti wrote:
>
> Hi Hervé,
>
> Now all builds pass – thanks for your help!
>
> As you mention we have a warning to iron out in the documentation and 
> we’ll also sneak in the other fixes to the documentation you are 
> kindly suggesting.
>
> Just to be sure, if I want these changes to appear in release 3.15 I 
> just need to push them to my Bioconductor master branch and don’t need 
> to create a RELEASE_3_15 branch, since that will automatically branch 
> off the latest master. Is this correct?
>
Yes

> Also, I don’t need to do anything else for this build to be propagated 
> to the users in version 3.14 since that happens automatically when the 
> build passes. Is this right?
>
Bumping the version is what triggers propagation. Note that we only 
build release (BioC 3.14) every other day, with reports on Mondays, 
Wednesdays, and Fridays. FWIW I don't see your latest changes on today's 
report, maybe because you pushed them after the builds started yesterday:

https://bioconductor.org/checkResults/3.14/bioc-LATEST/MoonlightR/

This means that they will show up on Friday's report, granted that you 
actually pushed them to the RELEASE_3_14 branch. If you also bumped the 
version (which you should do if you haven't yet), then the blue LEDs on 
the right will turn green indicating propagation of the new version 
(normally 1.20.1).

Cheers,

H.

> Best,
>
> Matteo
>
> *From: *Hervé Pagès <hpages.on.github using gmail.com>
> *Date: *Tuesday, 22 March 2022 at 21.23
> *To: *Matteo Tiberti <tiberti using cancer.dk>, bioc-devel using r-project.org 
> <bioc-devel using r-project.org>
> *Subject: *Re: [Bioc-devel] macOS auto build fails with "graphics API 
> version mismatch"
>
> Hi Matteo,
>
> On 21/03/2022 03:53, Matteo Tiberti wrote:
> > Dear all,
> >
> > I'm looking into the build failure of our MoonlightR package on 
> merida1 (macOS). It fails because vignettes fail to compile:
> >
> > Quitting from lines 532-546 (Moonlight.Rmd)
> > Error: processing vignette 'Moonlight.Rmd' failed with diagnostics:
> > Graphics API version mismatch
> > --- failed re-building �Moonlight.Rmd�
> >
> > The error refers to a function call that is supposed to generate an 
> image file for the vignette using ggsave.
> >
> > I have installed R-devel on macOS 10.15.7 and I am trying to 
> replicate the error, but it seems to build correctly on my system. 
> I've done some searching and I suspect that packages that use the 
> graphics API need to be recompiled on the build system since the API 
> version changed with R 4.2. Do you think this might be the case and, 
> if so, should I wait for this to be fixed on merida?
>
> This should have been taken care of now. Let us know if you still see
> this error on tomorrow's report.
>
> >
> > Notice that MoonlightR also doesn't build on Windows now because of 
> an unrelated issue with a dependency
>
> Looks like it's gone on today's report :-)
>
> BTW can you please remove MoonlightR/vignettes/Moonlight.html from the
> git repo of your package? The HTML vignette is automatically generated
> by 'R CMD build' and added to the resulting source tarball. As such it
> should not be pre-compiled and included in the package source tree.
>
> FWIW I get the following problem when running 'R CMD Stangle' on the
> markdown vignette:
>
>    hpages using spectre:~/MoonlightR/vignettes$ R CMD Stangle Moonlight.Rmd
>    Warning: The closing backticks on line 669 (" ```") in Moonlight.Rmd
> do not match the opening backticks "```" on line 667. You are
> recommended to fix either the opening or closing delimiter of the code
> chunk to use exactly the same numbers of backticks and same level of
> indentation (or blockquote).
> Output file:  Moonlight.R
>
> Maybe you want to look into this.
>
> Thanks,
>
> H.
>
> >
> > Thank you,
> >
> > Matteo Tiberti
> >
> > Danish Cancer Society
> > Strandboulevarden 49
> > DK-2100 Copenhagen
> > Telephone: +45 35 25 73 07
> >
> >
> > 
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> >
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> >
> >
> > _______________________________________________
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>
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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