From jeffrey.horner at gmail.com  Fri Nov 11 06:00:22 2011
From: jeffrey.horner at gmail.com (Jeffrey Horner)
Date: Thu, 10 Nov 2011 23:00:22 -0600
Subject: [Rd] When collected warnings exceeds 50
In-Reply-To: <CAD+yNFjt51Jch5XnnX-mXjzeAW7Qeqemha97SdmpL=qS2hgfMQ@mail.gmail.com>
References: <CAD+yNFjt51Jch5XnnX-mXjzeAW7Qeqemha97SdmpL=qS2hgfMQ@mail.gmail.com>
Message-ID: <CAD+yNFip_PJd18ZJZVNeVJ3bMB-2uNm_cuKsUna39S8mtgwU+A@mail.gmail.com>

On Thu, Nov 10, 2011 at 10:54 PM, Jeffrey Horner
<jeffrey.horner at gmail.com> wrote:
> Hi,
>
> I've been tracking down a memory leak in an rApache application,
> http://data.vanderbilt.edu/rapache/bbplot. The code was deployed in
> 2007 and has survived numerous upgrades of both R and rApache
> (including upgrades and bugs in RMySQL). It's written in such a way so
> that web crawlers will download every possible URL the app will
> create. It's not a high-traffic app, but just about every line of code
> is executed at some point during a crawl by Google, Bing, etc.
>
> Here's the salient point: the app (well, just about all rApache apps)
> sets option warn to 0 to collect all warnings until a request is
> completed. It turns out that some requests will collect more than 50
> warnings, and the result is an apache process that leaks memory until
> finally seg faulting somewhere in one of R's extra packages, if I
> recall correctly.
>
> After what seems like a month working on this problem, I think I've
> narrowed it down to a simple test case. I'm testing with R-devel
> r57624 on ubuntu linux. Running the following under valgrind:
>
> R -d valgrind
>> options(warn=0)
>> for (i in 1:51) factor(1,levels=c(1,1) # duplicate level warningcall

Missed a closing parenthesis. should be :

> options(warn=0)
> for (i in 1:51) factor(1,levels=c(1,1)) # duplicate level warningcall

>
> and you should see "Invalid read" messages. I've narrowed it down to
> vwarningcall_dflt starting a new R context via begincontext() ?but
> returning early without calling endcontext() in errors.c:
>
> ?svn diff src/main/errors.c
> Index: src/main/errors.c
> ===================================================================
> --- src/main/errors.c ? (revision 57624)
> +++ src/main/errors.c ? (working copy)
> @@ -333,8 +333,11 @@
> ? ? ? ?char *tr; int nc;
> ? ? ? ?if(!R_CollectWarnings)
> ? ? ? ? ? ?setupwarnings();
> - ? ? ? if( R_CollectWarnings > 49 )
> + ? ? ? if( R_CollectWarnings > 49 ) {
> + ? ? ? ? ? endcontext(&cntxt);
> + ? ? ? ? ? inWarning = 0;
> ? ? ? ? ? ?return;
> + ? ? ? }
> ? ? ? ?SET_VECTOR_ELT(R_Warnings, R_CollectWarnings, call);
> ? ? ? ?Rvsnprintf(buf, min(BUFSIZE, R_WarnLength+1), format, ap);
> ? ? ? ?if(R_WarnLength < BUFSIZE - 20 && strlen(buf) == R_WarnLength)
>
> This fix eliminates the "Invalid read" errors, but I'm unsure if it
> fixes my application. I'll find out tomorrow.
>
> Jeff
>



[Rd] When collected warnings exceeds 50
Jeffrey Horner