From mitomaster at gmail.com  Mon Dec 16 18:18:47 2013
From: mitomaster at gmail.com (Krzysztof Mlynarczyk)
Date: Mon, 16 Dec 2013 18:18:47 +0100
Subject: [Rd] External pointers and changing SEXPTYPE
In-Reply-To: <52AEE12F.1090506@stats.ox.ac.uk>
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	<CAPxYnfpj-Z0SNEFdNW33vr+GZLzD8nD_vCEUacfEUA0Mi_Q-9Q@mail.gmail.com>
	<52AEE12F.1090506@stats.ox.ac.uk>
Message-ID: <CAPxYnfp2btvLFUf9t6PQfToXqWVjBd5YXgnfTZresAZXk8ykjw@mail.gmail.com>

Yes, it turned out that using R_PreserveObject and R_ReleaseObject
solved that problem.
I sincerely apologize for posting only several chunks of code.
Fortunately for me, the descritpion I gave was sufficient to track
down what was missing.
Thank you very much!

Chris

2013/12/16 Prof Brian Ripley <ripley at stats.ox.ac.uk>:
> On 16/12/2013 11:07, Krzysztof Mlynarczyk wrote:
>>
>> As far as I understood the documentation, external pointer should be
>> automatically protected from gc when returned to environment. The
>
>
> Yes, but you didn't give us the complete reproducible example the posting
> guide asks for.  Peter's diagnosis is very likely right, but you have failed
> to give us anything like enough to go on.
>
>
>> solution you've just suggested would cause stack imbalance.
>
>
> It would not work anyway: the pointer stack top is reset when .Call (or
> similar) returns.
>
> There is R_PreserveObject for this purpose.
>
>
>> Recently I've been thinking of encapsulating the pointer into a nice
>> object using Rcpp. This sounds better that telling people to have fun
>> with an external pointer itself.
>>
>> KM
>>
>> 2013/12/16 peter dalgaard <pdalgd at gmail.com>:
>>>
>>> Offhand, I'd say that if "all protects get unprotected before return"
>>> mydata->ans is not protected against garbage collection, and thus very
>>> likely collected and reused. If mydata is created by Calloc, the GC has no
>>> way of knowing that it might have pointers to things that are intended to
>>> persist.
>>>
>>> I haven't played with external pointers for a while, but I'd expect that
>>> you'd need to retain a PROTECT on mydata->ans, and then UNPROTECT_PTR or so
>>> in the finalizer.
>>>
>>> -pd
>>>
>>> On 16 Dec 2013, at 04:11 , Krzysztof Mlynarczyk <mitomaster at gmail.com>
>>> wrote:
>>>
>>>> Dear Developers,
>>>>
>>>>
>>>> I've been struggling through writing R extension in C. I've been using
>>>> an external pointer to store my data (please see sample below). I
>>>> encountered a very weird erroneous behaviour: when I tried to use my
>>>> external pointer to a structure holding several types of data,
>>>> including SEXPs, I discovered that SEXPs change their types between
>>>> returning from initialization function and another one that uses the
>>>> pointer.
>>>>
>>>> sample R code:
>>>>
>>>> # initializing
>>>> a <- init_my_ptr(fname)
>>>>
>>>> # reading more data: error!
>>>> df <- read_my_data(a)
>>>>
>>>> data structure in C:
>>>> typedef struct {
>>>>   SEXP ans, ans_nms, R_z, R_a, R_b, R_c;
>>>>   FTYPE *datafile;
>>>>   char *fname;
>>>>   float *a, *b, *c;
>>>>   int f_type;
>>>>   float t, p, l;
>>>>   int st, na, result, bFlags;
>>>>   XXX z;
>>>> } my_data_ptr;
>>>>
>>>> // In a C function initializing the external pointer:
>>>> my_data_ptr *mydata = Calloc( 1, my_data_ptr ) ;
>>>> SEXP Rdata;
>>>> PROTECT(Rdata = R_MakeExternalPtr( mydata, R_fname, R_NilValue ));
>>>> ...
>>>> mydata->a = Calloc(mydata->na, float);
>>>> // same for b and c
>>>> // initializing names so that I could use e.g. df$a where df is
>>>> returned by read_my_data()
>>>> PROTECT(mydata->ans_nms = Rf_allocVector(STRSXP, efldNR ));
>>>>   for( ix = 0; ix < efldNR; ix++ )
>>>>     SET_STRING_ELT(mydata->ans_nms, ix, mkChar(vnames[ix]));
>>>>
>>>> // later I bind values of non-R variables from my data structure to a
>>>> proper vector
>>>> PROTECT(mydata->ans = Rf_allocVector(VECSXP, efldNR ));
>>>>
>>>>   Rf_setAttrib(mydata->ans, R_NamesSymbol, mytraj->ans_nms);
>>>>   SET_VECTOR_ELT(mydata->ans, 0,      mydata->R_a );
>>>>   SET_VECTOR_ELT(mydata->ans, 1,      mydata->R_b );
>>>> ...
>>>> // all protects get unprotected before return
>>>> // finalizer is registered as well
>>>> return Rdata;
>>>>
>>>> Later on in read_my_data() I read the pointer:
>>>> my_data_ptr *mydata = (my_data_ptr*) R_ExternalPtrAddr(Rdata);
>>>>
>>>> // and REAL(mydata->R_a) yields error since TYPEOF(mydata->R_a) is not
>>>> REALSXP as it should be but RAWSXP for some reason // (sometimes it's
>>>> STRSXP or INTSXP while it should always be REALSXP)
>>>> // The error message says:
>>>> // REAL() can only be applied to a 'numeric', not a 'raw'
>>>>
>>>> // mydata->ans is the object returned to R where all the data is made
>>>> available to R user:
>>>> return mydata->ans;
>>>>
>>>> // end of example code
>>>>
>>>> Could you please point the possible reasons for the error along with
>>>> the ways of fixing this issue? I've been trying in R-3.0.2, 3.0.1 and
>>>> even 2.15 -- the problem happens in each of them.
>>>>
>>>>
>>>> Regards,
>>>> Christopher
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>> --
>>> Peter Dalgaard, Professor
>>> Center for Statistics, Copenhagen Business School
>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> Phone: (+45)38153501
>>> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
>>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
> --
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] External pointers and changing SEXPTYPE
Krzysztof Mlynarczyk