[Rcpp-devel] Debugging intermittant vignette re-building failure

[William Dunlap]

--- re-building ‘lolog-ergm.Rmd’ using rmarkdown
Quitting from lines 69-75 (lolog-ergm.Rmd)
Error: processing vignette 'lolog-ergm.Rmd' failed with diagnostics:
unimplemented type (28) in 'duplicate'


I don't believe there is a type (*SXP) 28 in R.  This could be due to
memory misuse.
Have you tried running the R code in lolog-ergm.Rmd (and your unit tests)
in R
after setting gctorture(TRUE)?

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Tue, Jan 8, 2019 at 1:31 PM Fellows, Ian <ian.fellows at stat.ucla.edu>
wrote:

>
> Hi All,
>
> I have a package ( https://github.com/statnet/lolog |
> https://cran.r-project.org/web/packages/lolog/index.html ) that makes
> extensive use of Rcpp modules and passes module objects up and down between
> R and C++ regularly. I’ve used the package extensively in large simulation
> studies, and analyses where it has been stable.
>
> However, I have become aware of an intermittent failure to re-build the
> vignettes during R CMD check. I’ve only ever encountered the issue during
> check. Every once in a while I get WARNINGS like the following:
>
>
> -------
>
> * checking re-building of vignette outputs ... WARNING
> Error(s) in re-building vignettes:
>   ...
> --- re-building ‘lolog-ergm.Rmd’ using rmarkdown
> Quitting from lines 69-75 (lolog-ergm.Rmd)
> Error: processing vignette 'lolog-ergm.Rmd' failed with diagnostics:
> unimplemented type (28) in 'duplicate'
>
> --- failed re-building ‘lolog-ergm.Rmd’
>
> --- re-building ‘lolog-introduction.Rmd’ using rmarkdown
> --- finished re-building ‘lolog-introduction.Rmd’
>
> SUMMARY: processing the following file failed:
>   ‘lolog-ergm.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> -------
>
> or
>
> -------
>
> * checking re-building of vignette outputs ... [336s/452s] WARNING
> Error(s) in re-building vignettes:
>   ...
> --- re-building ‘lolog-ergm.Rmd’ using rmarkdown
> --- finished re-building ‘lolog-ergm.Rmd’
>
> --- re-building ‘lolog-introduction.Rmd’ using rmarkdown
> Quitting from lines 355-381 (lolog-introduction.Rmd)
> Error: processing vignette 'lolog-introduction.Rmd' failed with
> diagnostics:
> cannot coerce type 'environment' to vector of type 'any'
> --- failed re-building ‘lolog-introduction.Rmd’
>
> SUMMARY: processing the following file failed:
>   ‘lolog-introduction.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> -------
>
>
> I’ve attempted to isolate the problem to something of a smaller but have
> thus far been unsuccessful. Since this only happens occasionally, I thought
> it might have something to do with how I’m passing objects up and down (
> see for example:
> https://github.com/statnet/lolog/blob/master/inst/include/Model.h#L89 and
> https://github.com/statnet/lolog/blob/master/inst/include/util.h#L29 ),
> but that is just a shot in the dark.
>
> Does anyone have any insight as to how i might be able to better debug
> this or intuitions about what could be the cause? Is it possible to get a
> stack trace when rebuilding the vignettes?
>
> My apologies for the lack of a simple reproducible example.
>
> Sincerely,
> Ian Fellows
>
>
>
>
>
>
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