[R-pkg-devel] Package Vignette depends on Ensembl, server certificate issue?

[Jeff Newmiller]

Maybe use r.rsp?

https://blog.r-hub.io/2020/06/03/vignettes/
How to include my pre-print / cheatsheet as a PDF vignette?



On April 8, 2021 12:39:20 PM PDT, "Dr. Connie Brett" <connie using aggregate-genius.com> wrote:
>Hello,
>I have a package (DGEobj) that depends on the Ensembl service to look
>up information used to build the vignette.  My builds work fine on
>Travis, locally and on R-hub.  Occasionally I have seen blips with
>regard to internet-based resources not being available, and my vignette
>depends on a number of internet resources to get example datasets. 
>However when I submitted my package to CRAN today the failures Windows
>and Debian were that the server certificate verification failed ( SSL
>certificate problem: unable to get local issuer certificate).
>I’m not sure if there is something I can do about this or if this is
>considered a "false positive" per the email - it seems like a "wait and
>retry" issue.  I don’t want to be rude uploading the package again
>without a change or erroneously emailing in response to the rejection. 
>How should this be handled properly now and into the future?  It isn’t
>feasible to not use Ensembl for this vignette.
>Thanks for your insight and feedback!
>
>Flavor: r-devel-windows-ix86+x86_64
>Check: re-building of vignette outputs, Result: WARNING
> Error(s) in re-building vignettes:
> --- re-building 'DGEobj_Overview.Rmd' using rmarkdown
>
> Ensembl site unresponsive, trying asia mirror
> Quitting from lines 259-280 (DGEobj_Overview.Rmd) 
>Error: processing vignette 'DGEobj_Overview.Rmd' failed with
>diagnostics:
> SSL certificate problem: unable to get local issuer certificate
> --- failed re-building 'DGEobj_Overview.Rmd'
>
> SUMMARY: processing the following file failed:
>   'DGEobj_Overview.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>
>
>Flavor: r-devel-linux-x86_64-debian-gcc
>Check: re-building of vignette outputs, Result: WARNING
> Error(s) in re-building vignettes:
> --- re-building 'DGEobj_Overview.Rmd' using rmarkdown
>
> Ensembl site unresponsive, trying asia mirror
> Quitting from lines 235-256 (DGEobj_Overview.Rmd) 
>Error: processing vignette 'DGEobj_Overview.Rmd' failed with
>diagnostics:
> server certificate verification failed. CAfile: none CRLfile: none
> --- failed re-building 'DGEobj_Overview.Rmd'
>
> SUMMARY: processing the following file failed:
>   'DGEobj_Overview.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>	[[alternative HTML version deleted]]
>
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-- 
Sent from my phone. Please excuse my brevity.