[R-pkg-devel] irrecoverable exception occurred during CRAN submission checks

[Daniel Lüdecke]

Hello,

I just submitted an update of my package to CRAN and it does not pass
incoming checks. While local checks, win-builder and GitHub CI
(Mac/Win/Linux) all pass, I get the Note you see below for the checks during
submission process. I have no idea why this happens and see this message for
the first time. I *assume* it's a temporary issue / false positive, but want
to be sure before I reply to the CRAN team.

Can anyone help how I can address this issue, or if it indeed might be a
false positive?

Thanks and best wishes
Daniel

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
  Maintainer: 'Daniel Lüdecke '

Flavor: r-devel-linux-x86_64-debian-gcc
Check: dependencies in R code, Result: NOTE
  
   *** caught segfault ***
  address 0x7f1c76752008, cause 'invalid permissions'
  
  Traceback:
   1: dyn.load(file, DLLpath = DLLpath, ...)
   2: library.dynam(lib, package, package.lib)
   3: loadNamespace(p)
   4: withCallingHandlers(expr, message = function(c) if (inherits(c,
classes)) tryInvokeRestart("muffleMessage"))
   5: suppressMessages(loadNamespace(p))
   6: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
   7: suppressWarnings(suppressMessages(loadNamespace(p)))
   8: doTryCatch(return(expr), name, parentenv, handler)
   9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))),
error = function(e) e)
  12: tools:::.check_packages_used(package = "insight")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault

--

_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg | www.uke.de
Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
_

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Re: [R-pkg-devel] Including fonts in an rmarkdown vignette

[David Hugh-Jones]

Thank you for these suggestions. Google fonts sounds like quite an easy
approach.
David


On Wed, 3 Jun 2020 at 10:03, David Gohel  wrote:

> David
>
> If you are ok to use one of the fonts available on google font, you could
> use package gfonts (in Suggests):
> https://cran.r-project.org/web/packages/gfonts/vignettes/gfonts.html
>
> As it will be « inline », your document size could inflate (I guess it
> could be an issue with CRAN) - if only one font, size should be ok.
>
> Otherwise, you also could add a css chunk to import the font from a public
> server - if no internet connexion, nothing will break.
>
> David
>
>
> Le 3 juin 2020 à 08:46, Maëlle SALMON via R-package-devel <
> r-package-devel@r-project.org> a écrit :
>
> Hi,
>
> I've recently seen an example of a package that provides its own fonts for
> a vignette. See links in
> https://blog.r-hub.io/2020/06/03/vignettes/#pretty-vignettes
>
>
> In that same post I link to a workaround I saw on this list
> https://www.mail-archive.com/r-package-devel@r-project.org/msg02921.html
> for changing the vignette format based on the versions of dependencies.
> Maybe something similar is possible for fonts (I have no idea).
>
> Maëlle.
>
> Den tisdag 2 juni 2020 20:14:24 CEST, David Hugh-Jones <
> davidhughjo...@gmail.com> skrev:
>
>
>
>
>
> Hi,
>
> I'd like to build a rmarkdown vignette with my own choice of fonts – I'm
> pernickety about look and feel.
>
> R CMD check will rebuild vignettes in the vignettes/ directory, and if
> relevant fonts aren't on the build machine, it'll give a warning.
>
> Here are the options I can think of:
> * build vignettes on my machine and put them in inst/doc. Don't mention the
> specific fonts in the Rmd file in vignettes/. So the file built by "R CMD
> check" won't look quite like the pre-built version.  This might work, but
> it seems against open source principle.
> * put font files in vignettes/ and refer to them in the rmarkdown file. I'm
> not sure how to do this.
> * limit myself to the fonts preinstalled on win-builder or CRAN machines.
> I'm not sure what these are
>
> Has anyone got any advice or examples?
>
> Cheers,
> David
>
> [[alternative HTML version deleted]]
>
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>
>
>

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Re: [R-pkg-devel] Including fonts in an rmarkdown vignette

[David Gohel]

David

If you are ok to use one of the fonts available on google font, you could use 
package gfonts (in Suggests):
https://cran.r-project.org/web/packages/gfonts/vignettes/gfonts.html 


As it will be « inline », your document size could inflate (I guess it could be 
an issue with CRAN) - if only one font, size should be ok.

Otherwise, you also could add a css chunk to import the font from a public 
server - if no internet connexion, nothing will break.

David


> Le 3 juin 2020 à 08:46, Maëlle SALMON via R-package-devel 
>  a écrit :
> 
> Hi,
> 
> I've recently seen an example of a package that provides its own fonts for a 
> vignette. See links in 
> https://blog.r-hub.io/2020/06/03/vignettes/#pretty-vignettes 
> 
> 
> In that same post I link to a workaround I saw on this list 
> https://www.mail-archive.com/r-package-devel@r-project.org/msg02921.html for 
> changing the vignette format based on the versions of dependencies. Maybe 
> something similar is possible for fonts (I have no idea).
> 
> Maëlle.
> 
> Den tisdag 2 juni 2020 20:14:24 CEST, David Hugh-Jones 
>  skrev: 
> 
> 
> 
> 
> 
> Hi,
> 
> I'd like to build a rmarkdown vignette with my own choice of fonts – I'm
> pernickety about look and feel.
> 
> R CMD check will rebuild vignettes in the vignettes/ directory, and if
> relevant fonts aren't on the build machine, it'll give a warning.
> 
> Here are the options I can think of:
> * build vignettes on my machine and put them in inst/doc. Don't mention the
> specific fonts in the Rmd file in vignettes/. So the file built by "R CMD
> check" won't look quite like the pre-built version.  This might work, but
> it seems against open source principle.
> * put font files in vignettes/ and refer to them in the rmarkdown file. I'm
> not sure how to do this.
> * limit myself to the fonts preinstalled on win-builder or CRAN machines.
> I'm not sure what these are
> 
> Has anyone got any advice or examples?
> 
> Cheers,
> David
> 
> [[alternative HTML version deleted]]
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> __
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Re: [R-pkg-devel] Including fonts in an rmarkdown vignette

[Maëlle SALMON via R-package-devel]

Hi,

I've recently seen an example of a package that provides its own fonts for a 
vignette. See links in 
https://blog.r-hub.io/2020/06/03/vignettes/#pretty-vignettes 


In that same post I link to a workaround I saw on this list 
https://www.mail-archive.com/r-package-devel@r-project.org/msg02921.html for 
changing the vignette format based on the versions of dependencies. Maybe 
something similar is possible for fonts (I have no idea).

Maëlle.

Den tisdag 2 juni 2020 20:14:24 CEST, David Hugh-Jones 
 skrev: 





Hi,

I'd like to build a rmarkdown vignette with my own choice of fonts – I'm
pernickety about look and feel.

R CMD check will rebuild vignettes in the vignettes/ directory, and if
relevant fonts aren't on the build machine, it'll give a warning.

Here are the options I can think of:
* build vignettes on my machine and put them in inst/doc. Don't mention the
specific fonts in the Rmd file in vignettes/. So the file built by "R CMD
check" won't look quite like the pre-built version.  This might work, but
it seems against open source principle.
* put font files in vignettes/ and refer to them in the rmarkdown file. I'm
not sure how to do this.
* limit myself to the fonts preinstalled on win-builder or CRAN machines.
I'm not sure what these are

Has anyone got any advice or examples?

Cheers,
David

    [[alternative HTML version deleted]]

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Re: [R-pkg-devel] [R] a question of etiquette

[Ivan Krylov]

On Tue, 2 Jun 2020 20:33:56 -0400
Avraham Adler  wrote:

> If there is a term which reflects that mechanism from a discipline
> other than biology, please let me know.

I think that "copyleft" is the term you are looking for. The Wikipedia
page [*] defines it as

>> the practice of offering people the right to freely distribute copies
>> and modified versions of a work with the stipulation that the same
>> rights be preserved in derivative works created later

-- 
Best regards,
Ivan

[*] https://en.wikipedia.org/wiki/Copyleft

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