Return a list from a .Call but segfaults

Sat, Sep 19, 2009 9:04 PM

After some examination, this is what i found (i changed the code
somewhat, i dont modify rawdata anymore)

load("/tmp/v.Rdata")
dyn.load("/ln/meraki/custom/lib64/R/library/mylib/libs/lib.so")
v=.Call("returnListOfKV",rawkv,numread)

## v is a list of 28231 lists each of length 2
j=v[1:10000] ; u=list();u=append(u,j)
and
 j=v[1:15164] ; u=list();u=append(u,j)
both work but for n> 15164
 j=v[1:n] ; u=list();u=append(u,j)
returns
Error: protect(): protection stack overflow

I have no idea why...
Regards
Saptarshi




On Sat, Sep 19, 2009 at 10:15 PM, Saptarshi Guha

<saptarshi.guha at gmail.com> wrote:

Hello,
I call a function via .Call passing to it a raw vector(D) and an integer(I)
The vector is a series ?K1,KData1, V1,VData1, K2, KData2, ...
where the integer K1 is the length of Data1 and similarly for Ki (wrt
Datai)(similarly for V*) There 2*I such pairs( (Ki,KDatai), (Vi,VDatai))

The numbers Ki(and Vi) are written in network order.

I am returning a list of I elements each element a list of two elements
corresponding to KData and VData (which are serialized R objects) .

?ll <- .Call("returnListOfKV", rawkv, numread)

When use the function with browser(), and type head(ll) i get valid results.
However, i get a segfault when the code runs the next line

?j <- append(j,ll)

(where j was defined as vector(mode='list') )

The code below looks alright, but it appears to crash when getting copied.
Now one could blame message2rexp (in kk_), but once in R, the result of
.Call is assigned to ll, everything should be protected.
In fact, if in kk_ i simply return a VECSXP with 2 elements, no errors, so
one could conclude that message2rexp is to blame.

Yet, when i replace the code with R code, that is using readBin and only
calling calling C(to call message2rexp) to deserialize a raw vector, I get
no such error.

There is something I'm missing , could someone tell me where?
Thank you for your time
Regards
Saptarshi


=== Using GDB? ====
I would like to run it through gdb, i get the following message
[Thread debugging using libthread_db enabled]
Error while reading shared library symbols:
Cannot find new threads: generic error
Cannot find new threads: generic error]

and cannot proceed.

==== Code ====
?SEXP returnListOfKV(SEXP raw,SEXP numread){

? ?if(TYPEOF(raw)!=RAWSXP){
? ? ?return(R_NilValue);
? ?}
? ?int num = INTEGER(numread)[0];
? ?char *rawdata = (char*)RAW(raw);
? ?SEXP KV ,rval;
? ?int r;
? ?PROTECT(rval = Rf_allocVector(VECSXP, num));
? ?for(int i=0;i<num;i++){
? ? ?SEXP k = R_NilValue;
? ? ?PROTECT(KV = Rf_allocVector(VECSXP, 2));

? ? ?r = reverseUInt(*((int*) rawdata)); //converts network order to host
? ? ?rawdata+=4; //yes, hard code size of int
? ? ?PROTECT(k= kk_(rawdata,r)); //deserializes data and returns a SEXP
? ? ?rawdata+= r;
? ? ?SET_VECTOR_ELT(KV,0, k);
? ? ?UNPROTECT(1);

? ? ?r = reverseUInt(*((int*) rawdata));
? ? ?rawdata+=4;
? ? ?PROTECT(k= kk_(rawdata,r));
? ? ?rawdata+=r;
? ? ?SET_VECTOR_ELT(KV,1, k);
? ? ?UNPROTECT(1);

? ? ?SET_VECTOR_ELT(rval,i,KV);
? ? ?UNPROTECT(1);
? ?}
? ?UNPROTECT(1);
? ?return(rval);
?}


?SEXP kk_(char *d,int n){
? ?SEXP k;
? ?REXP *rexp = new REXP();
? ?rexp->Clear();
? ?rexp->ParseFromArray(d,n);
? ?PROTECT(k = message2rexp(*rexp));
? ?delete(rexp);
? ?UNPROTECT(1);
? ?return(k);
?}

Saptarshi Guha | saptarshi.guha at gmail.com |
http://www.stat.purdue.edu/~sguha

Return a list from a .Call but segfaults

Thread (3 messages)