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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:
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* 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
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or
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* 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
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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