[Rcpp-devel] "Error during wrapup"

John Mous john.mous0 at gmail.com
Thu May 29 00:35:30 CEST 2014


No luck with gctorture on yet, but I haven't run it for very long. It
slowed things down to a complete crawl, but maybe in the long run it can
recreate the problem faster than running the original code (about 12 hours,
the previous estimate of a day was too high), so this may still be
worthwhile.

On a whim I did try changing the two instances of Shield to Armor this
morning (I was able to locate the code in wrap.h by digging around before I
saw your e-mail) and ran the original full code without gctorture on, and
the problem still persists.


On Wed, May 28, 2014 at 3:44 PM, Romain Francois
<romain at r-enthusiasts.com>wrote:

> (now with some links):
>
> Le 28 mai 2014 à 16:31, John Mous <john.mous0 at gmail.com> a écrit :
>
> The object really is just built as part of the return statement. i.e. the
> lines from my prior e-mail exist as-is in the full code,
>
>
> Sure. What happens is that Rcpp::export generates something that calls
> wrap( std::map<std::string,int> ).
>
> there's just more that actually builds the variables X1-X4 beforehand.
>
>
> It should not be relevant.
>
> So I'm not sure where to debug from the client side. I'm a C/C++
> developer, but have no experience with Rcpp internals or the general
> interface between R and C. I can insert some debug statements on the Rcpp
> side if you can guide me to where wrap is defined.
>
>
> well wrap is defined here:
>
> https://github.com/RcppCore/Rcpp/blob/master/inst/include/Rcpp/internal/wrap_end.h#L28
>
> It then performs a series of dispatch, that eventually lead to something
> that handles std::map<std::string,int>:
>
> https://github.com/RcppCore/Rcpp/blob/master/inst/include/Rcpp/internal/wrap.h#L255
>
> template <typename InputIterator, typename T>
> inline SEXP range_wrap_dispatch___impl__cast( InputIterator first, InputIterator last, ::Rcpp::traits::false_type ){
> 	size_t size = std::distance( first, last ) ;
> 	const int RTYPE = ::Rcpp::traits::r_sexptype_traits<typename T::second_type>::rtype ;
> 	Shield<SEXP> x( Rf_allocVector( RTYPE, size ) );
> 	Shield<SEXP> names( Rf_allocVector( STRSXP, size ) ) ;
> 	typedef typename ::Rcpp::traits::storage_type<RTYPE>::type CTYPE ;
> 	CTYPE* start = r_vector_start<RTYPE>(x) ;
> 	size_t i =0;
> 	std::string buf ;
> 	for( ; i<size; i++, ++first){
> 		start[i] = (*first).second ;
> 		buf = (*first).first ;
> 		SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
> 	}
> 	::Rf_setAttrib( x, R_NamesSymbol, names ) ;
> 	return wrap_extra_steps<T>( x ) ;
> }
>
>
> what I suspect to be the problem is this line:
>
>  ::Rf_setAttrib( x, R_NamesSymbol, names ) ;
>
>
> What Romain says makes sense to me, despite my lack of expertise in this
> area.. the really intermittent nature of the problem and the fact that I
> can't recreate it in a small / fast running example suggests that perhaps
> this manifests when R happens to garbage collect at an unfortunate time (if
> I understood correctly). Thanks again.
>
>
> Something like that. as hadley hinted, please try this under gc torture,
> or preferably through a debugger.
>
> On Wed, May 28, 2014 at 10:12 AM, Dirk Eddelbuettel <edd at debian.org>wrote:
>
>>
>> On 28 May 2014 at 10:02, John Mous wrote:
>> | Hmm, unfortunately the GitHub version failed also.
>>
>> Darn.
>>
>> | The attributes on the failed
>> | object are a little different though, here's what they look like:
>> |
>> | Browse[1]> str(results)
>> |  atomic [1:4] 1 1 2270 0
>> |  - attr(*, "")= symbol sim
>> |  - attr(*, "value")= promise to  NULL
>>
>> I am not sure what we can do without a reproducible example. :-/
>> The code just got a review / refreshment over the last few months.
>>
>> You best bet may the slow and tedious insertion of debug statements to see
>> when / if the object changes.
>>
>> Dirk
>>
>> --
>> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>>
>
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