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

[Fellows, Ian]

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