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

[Dr. Connie Brett]

Thank you for pointing me to this resource, works like a charm!

> On Apr 9, 2021, at 12:14 AM, Jeff Newmiller <jdnewmil using dcn.davis.ca.us> wrote:
> 
> 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.