From jeff.horner at vanderbilt.edu  Wed Jul 16 17:17:41 2008
From: jeff.horner at vanderbilt.edu (Jeffrey Horner)
Date: Wed, 16 Jul 2008 10:17:41 -0500
Subject: [Rd] Embedded R, last errormessage, and stack smashing
In-Reply-To: <27d1e6020807160602h52fa23a0v6651dad365b5f00b@mail.gmail.com>
References: <27d1e6020806300448r10d55c38jd6400c923e5a74cc@mail.gmail.com>
	<27d1e6020807160602h52fa23a0v6651dad365b5f00b@mail.gmail.com>
Message-ID: <487E1115.2020207@vanderbilt.edu>

Laurent Gautier wrote on 07/16/2008 08:02 AM:
> The only way to overcome the problem I can find is to tweak the
> R_CStackLimit with:
> 
> R_CStackLimit = (uintptr_t) -1;
> 
> The question I am having now is: what are the implications of doing
> so, that is what are the potential problems ?

The problem is a program crash without saving data. Stack overflow is 
usually caused by either infinite recursion or very large stack (i.e. 
local) variables.

I've always disabled stack checking in rapache, and I never knew why the 
checking was added to R, but again wikipedia has merit:

http://en.wikipedia.org/wiki/Stack_overflow

Jeff

> 
> The R-extensions manual says:
> " Stack-checking can be disabled by seting R_CStackLimit =
> (uintptr_t)-1, but it is better to
> if possible set appropriate values. (What these are and how to
> determine them are OS-specific,
> and the stack size limit may differ for secondary threads. If you have
> a choice of stack size, at
> least 8Mb is recommended.)"
> I am not very sure of how an appropriate value can be determined.
> 
> I looked around, and the JRI (Java/R Interface) is just disabling
> stack checking for example.
> 
> 
> Thanks,
> 
> 
> Laurent
> 
> 
> 2008/6/30 Laurent Gautier <lgautier at gmail.com>:
>> Dear list,
>>
>> I am having an embedded R, dying with
>> *** stack smashing detected *** in one specific case.
>>
>> My code is such as I evaluate R expression with C code like
>>
>> res = R_tryEval(expr, env, &error);
>>
>> and in case of error, get the error message (usually sucessfully) with
>> code like below:
>>
>> SEXP geterrmessage = findVar(install("geterrmessage"), R_BaseNamespace);
>> PROTECT(expr = allocVector(LANGSXP, 1));
>> SETCAR(expr, geterrmessage);
>> PROTECT(res = Rf_eval(expr, R_GlobalEnv));
>> // ---> *** stack smashing detected ***
>>
>> The call to Rf_eval does not return as the stack smashing error stops the show.
>>
>> Tracing with gdb where the problem occurs, I follow the path:
>> eval -> R_CheckStack in main/error.c -> errorcall in main/error.c
>>
>>
>> In errorcall, I narrow down the origin of the problem around the lines:
>> 658    va_start(ap, format);
>> 659    verrorcall_dflt(call, format, ap);
>> 660    va_end(ap);
>> and add a breakpoint on each one of those lines.
>>
>>
>> My gdb session till the stack smashing crashing is then looking like:
>>
>> Breakpoint 7, Rf_errorcall (call=0x828ef8, format=0x7f4dbdc87698 "C
>> stack usage is too close to the limit")
>>    at errors.c:658
>> 658         va_start(ap, format);
>> (gdb) p ap
>> $2 = {{gp_offset = 16, fp_offset = 48, overflow_arg_area = 0x41c22f60,
>> reg_save_area = 0x41c22e70}}
>> (gdb) p format
>> $3 = 0x7f4dbdc87698 "C stack usage is too close to the limit"
>> (gdb) continue
>> Continuing.
>>
>> Breakpoint 8, Rf_errorcall (call=0x828ef8, format=0x7f4dbdc87698 "C
>> stack usage is too close to the limit")
>>    at errors.c:659
>> 659         verrorcall_dflt(call, format, ap);
>> (gdb) continue
>> Continuing.
>>
>> Breakpoint 6, Rf_errorcall (call=0x828ef8, format=0x7f4dbdc87406 "%s")
>> at errors.c:648
>> 648         if (R_ErrorHook != NULL) {
>> (gdb) continue
>> Continuing.
>>
>> Breakpoint 7, Rf_errorcall (call=0x828ef8, format=0x7f4dbdc87406 "%s")
>> at errors.c:658
>> 658         va_start(ap, format);
>> (gdb) continue
>> Continuing.
>>
>> Breakpoint 8, Rf_errorcall (call=0x828ef8, format=0x7f4dbdc87406 "%s")
>> at errors.c:659
>> 659         verrorcall_dflt(call, format, ap);
>> (gdb) continue
>> Continuing.
>> *** stack smashing detected ***: /usr/bin/python terminated
>>
>>
>> My understanding is that there is a C stack problem about to happen R
>> tries to report, but in the process of reporting it
>> causes a C stack-related crash. Is there something odd with R handling
>> the situation, or should I look for the cause
>> of the problem elsewhere ?
>>
>> Thanks,
>>
>>
>> L.
>>
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
http://biostat.mc.vanderbilt.edu/JeffreyHorner



[Rd] Embedded R, last errormessage, and stack smashing
Jeffrey Horner