From hb at biostat.ucsf.edu  Thu Sep 29 23:34:50 2011
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Thu, 29 Sep 2011 14:34:50 -0700
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: <CAFDcVCRNqfMcRdh+-onLT3gVZc6HjgBNhpax_rBWS_Ya7FYivQ@mail.gmail.com>

On Thu, Sep 29, 2011 at 2:00 PM, Jeffrey Horner
<jeffrey.horner at gmail.com> 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.

With R devel (2011-09-28 r57099) and R v2.13.1 patched (2011-09-05
r56953) on Windows 7 64-bit you get:

> grep("[^[:blank][:cntrl]]","\\n",perl=TRUE)
integer(0)

/Henrik

>
> 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)
>
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>



[Rd] grep and PCRE fun
Henrik Bengtsson