From schlather at math.uni-goettingen.de  Wed Jan 28 00:49:20 2009
From: schlather at math.uni-goettingen.de (Martin Schlather)
Date: Wed, 28 Jan 2009 00:49:20 +0100
Subject: [Rd] uninitialised value in R (PR#13476)
In-Reply-To: <497F4C92.1060606@epfl.ch>
References: <20090127152007.9980A282EFF8@mail.pubhealth.ku.dk>
	<497F4C92.1060606@epfl.ch>
Message-ID: <497F9D80.2050102@math.uni-goettingen.de>

Hi Mathieu,

Very strange.
(i) The whole package RandomFields is written with ` extern "C" '
    and seems working. There is no message from valgrind
    anywhere, except in two situations that I have boiled
    down to the code in the bug report.
(ii) without ` extern "C" ' I get a warning plus an
    error:

> .Call("XXX")
==18032== Conditional jump or move depends on uninitialised value(s)
==18032==    at 0x401620C: (within /lib/ld-2.8.so)
==18032==    by 0x42825C3: (within /lib/libc-2.8.so)
==18032==    by 0x4282989: _dl_sym (in /lib/libc-2.8.so)
==18032==    by 0x417ADE7: (within /lib/libdl-2.8.so)
==18032==    by 0x400DE25: (within /lib/ld-2.8.so)
==18032==    by 0x417B0DB: (within /lib/libdl-2.8.so)
==18032==    by 0x417AD72: dlsym (in /lib/libdl-2.8.so)
==18032==    by 0x811012D: R_dlsym (Rdynload.c:787)
==18032==    by 0x8110A98: R_FindSymbol (Rdynload.c:836)
==18032==    by 0x816E41C: resolveNativeRoutine (dotcode.c:240)
==18032==    by 0x817473A: do_dotcall (dotcode.c:825)
==18032==    by 0x8194C12: Rf_eval (eval.c:487)
==18032==    by 0x805B163: Rf_ReplIteration (main.c:257)
==18032==    by 0x805B3E7: R_ReplConsole (main.c:306)
==18032==    by 0x805B6D7: run_Rmainloop (main.c:966)
==18032==    by 0x8058F80: main (Rmain.c:33)
Error in .Call("XXX") : C symbol name "XXX" not in load table

Have you named the file u.c or u.cc?

Cheers,
Martin


Mathieu Ribatet wrote:
> Hi Martin,
> 
> I wasn't able to compile your files. Replacing "extern "C" SEXP XXX();"
> by "SEXP XXX();" solve the issue and I got no message from valgrind -
> I'm not sure this is what you really want to do though.
> I hope this might help.
> Cheers,
> Mathieu
> 
> 
> schlather at math.uni-goettingen.de a ?crit :
>> Hi,
>>
>> I get an "Conditional jump or move depends on uninitialised value(s)"
>> from valgrind when using 'solve' in combination with some simple
>> C-code. (I did not use other functions of R besides 'solve'.)
>>
>> In detail: running
>>
>> R --vanilla -d "valgrind --tool=memcheck --memcheck:leak-check=yes
>> --num-callers=20 "
>>
>> and calling
>>
>> .Call("XXX")
>> nd <- 3
>> solve(diag(nd) , as.vector(1:nd))
>> .Call("XXX")
>>
>> gives the above valgrind message for the second call of "XXX".
>> Without "solve" in the middle, there is no message
>> from valgrind.
>>
>> Best regards,
>> Martin
>>
>>
>> /////////////////////////////// C source file u.cc
>> #include "u.h"
>>
>> SEXP XXX() {
>>   SEXP ans;
>>   PROTECT (ans = allocVector(INTSXP, 1));
>>   INTEGER(ans)[0] = 1;
>>   UNPROTECT(1);
>>   return ans;
>> }
>>
>>
>> /////////////////////////////// header file u.h
>> #ifndef RFsimu_public_H
>> #define RFsimu_public_H 1
>>
>> #include <R.h>
>> #include <Rinternals.h>
>> #include <Rmath.h>
>> #include <Rdefines.h>
>>
>> extern "C" SEXP XXX();
>>
>>
>> #endif /* RF_simu_PUBLIC_H*/
>>
>>
>>
>>
>>
>>
>> --please do not edit the information below--
>>
>> Version:
>>  platform = i686-pc-linux-gnu
>>  arch = i686
>>  os = linux-gnu
>>  system = i686, linux-gnu
>>  status = Under development (unstable)
>>  major = 2
>>  minor = 9.0
>>  year = 2009
>>  month = 01
>>  day = 13
>>  svn rev = 47573
>>  language = R
>>  version.string = R version 2.9.0 Under development (unstable)
>> (2009-01-13 r47573)
>>
>> Locale:
>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>>
>>
>> Search Path:
>>  .GlobalEnv, package:stats, package:graphics, package:grDevices,
>> package:utils, package:datasets, package:methods, Autoloads, package:base
>>
>>   
> 


-- 
Prof. Dr. Martin Schlather
Institut f?r Mathematische Stochastik & Zentrum f?r Statistik
Georg-August-Universit?t G?ttingen
Goldschmidtstr. 7, 5.111
D -- 37077 G?ttingen

schlather at math.uni-goettingen.de
http://www.stochastik.math.uni-goettingen.de/~schlather
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phone: +49 (0)551 39 17 2131       fax : +49 (0)551 39 13 505



[Rd] uninitialised value in R (PR#13476)
Martin Schlather