From simon.urbanek at r-project.org  Fri Sep 30 17:04:21 2011
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Fri, 30 Sep 2011 11:04:21 -0400
Subject: [Rd] grep and PCRE fun
In-Reply-To: <CAD+yNFjsZcddyJ6KPuOfW93PLfoz7wzeGhX+iKt7s5wv=_0TZg@mail.gmail.com>
References: <CAD+yNFjsZcddyJ6KPuOfW93PLfoz7wzeGhX+iKt7s5wv=_0TZg@mail.gmail.com>
Message-ID: <DF520E23-2EE0-4BED-9F6C-9245F4958FF0@r-project.org>

Jeff,

this is really a bug in PCRE since the length (0) is a multiple of 3 as documented so PCRE should not be writing anything. Anyway, this has been now fixed (by Brian).

Cheers,
Simon


On Sep 29, 2011, at 5:00 PM, Jeffrey Horner wrote:

> Hello,
> 
> I think I've found a bug in the C function do_grep located in
> src/main/grep.c. It seems to affect both the latest revisions of
> R-2-13-branch and trunk when compiling R without optimizations and
> with it's own version of pcre located in src/extra, at least on ubuntu
> 10.04.
> 
> According to the pcre_exec API (I presume the later versions), the
> ovecsize argument must be a multiple of 3 , and the ovector argument
> must point to a location that can hold at least ovecsize integers. All
> the pcre_exec calls made by do_grep, save one, honors this. That one
> call seems to overwrite areas of the stack it shouldn't. Here's the
> smallest example I found that tickles the bug:
> 
>> grep("[^[:blank][:cntrl]]","\\n",perl=TRUE)
> Error in grep("[^[:blank][:cntrl]]", "\\n", perl = TRUE) :
>  negative length vectors are not allowed
> 
> As described above, this error occurs on ubuntu 10.04 when R is
> compiled without optimizations ( I typically use CFLAGS="-ggdb"
> CXXFLAGS="-ggdb" FFLAGS="-ggdb" ./configure --enable-R-shlib), and the
> pcre_exec call executed from do_get overwrites the integer nmatches
> and sets it to -1. This has the effect of making do_grep try and
> allocate a results vector of length -1, which of course causes the
> error message above.
> 
> I'd be interested to know if this bug happens on other platforms.
> 
> Below is my simple fix for R-2-13-branch (a similar fix works for
> trunk as well).
> 
> Jeff
> 
> $ svn diff main/grep.c
> Index: main/grep.c
> ===================================================================
> --- main/grep.c	(revision 57110)
> +++ main/grep.c	(working copy)
> @@ -723,7 +723,7 @@
> {
>     SEXP pat, text, ind, ans;
>     regex_t reg;
> -    int i, j, n, nmatches = 0, ov, rc;
> +    int i, j, n, nmatches = 0, ov[3], rc;
>     int igcase_opt, value_opt, perl_opt, fixed_opt, useBytes, invert;
>     const char *spat = NULL;
>     pcre *re_pcre = NULL /* -Wall */;
> @@ -882,7 +882,7 @@
> 	    if (fixed_opt)
> 		LOGICAL(ind)[i] = fgrep_one(spat, s, useBytes, use_UTF8, NULL) >= 0;
> 	    else if (perl_opt) {
> -		if (pcre_exec(re_pcre, re_pe, s, strlen(s), 0, 0, &ov, 0) >= 0)
> +		if (pcre_exec(re_pcre, re_pe, s, strlen(s), 0, 0, ov, 3) >= 0)
> 		    INTEGER(ind)[i] = 1;
> 	    } else {
> 		if (!use_WC)
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 



[Rd] grep and PCRE fun
Simon Urbanek