From charlie at stat.umn.edu  Wed Aug  3 02:03:34 2005
From: charlie at stat.umn.edu (Charles Geyer)
Date: Tue, 2 Aug 2005 19:03:34 -0500
Subject: [Rd] valgrind complains about regex.c (PR#8043)
In-Reply-To: <Pine.LNX.4.61.0508020704180.19394@gannet.stats>
References: <20050801212527.C2689A75B@slim.kubism.ku.dk>
	<Pine.LNX.4.61.0508020704180.19394@gannet.stats>
Message-ID: <20050803000334.GB6364@stat.umn.edu>

On Tue, Aug 02, 2005 at 07:13:54AM +0100, Prof Brian Ripley wrote:
> Did you compile R without optimization?  Such reads are often the result 
> of read-aheads produced by the optimizer in an attempt to keep 
> pipelines full (and are harmless).

    linux$ R CMD config CFLAGS
    -g -O2

so no.  I just took the defaults.  I'll try that too along with R-patched.

> 
> On an un-optimized build of R I am unable to reproduce this.  (I also was 
> unable to reproduce it on my optimized build of 2.1.1 using gcc 3.4.4, 
> although I did get a report on other read-aheads.)
> 
> On Mon, 1 Aug 2005 charlie at stat.umn.edu wrote:
> 
> >I think I am using objects according to the man page.
> >This seems to be a valid regular expression.  But whether
> >I know what I'm doing or no, it still shouldn't be doing
> >what valgrind seems to be saying it's doing.  (IMHO)
> 
> I think you need to take that up with compiler designers: it is common 
> practice.
> 
> >---------- start of script ----------
> >Script started on Mon 01 Aug 2005 02:09:00 PM PDT
> >linux$ printenv VALGRIND_OPTS
> >--tool=3Dmemcheck
> >linux$ cat bar.R
> >
> >foo <- 1
> >bar <- 2:3
> >baz <- 4:6
> >qux <- matrix(7:10, 2)
> >
> >ls()
> >rm(list =3D objects(pattern =3D "^[a-pr-z]"))
> >ls()
> >
> >linux$ R --version
> >R 2.1.1 (2005-06-20).
> >Copyright (C) 2005 R Development Core Team
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under the terms of the GNU
> >General Public License.  For more information about these matters,
> >see http://www.gnu.org/copyleft/gpl.html.
> >linux$ gcc --version
> >=1B[0mgcc (GCC) 3.3.5 20050117 (prerelease) (SUSE Linux)
> >=1B[0mCopyright (C) 2003 Free Software Foundation, Inc.
> >=1B[0mThis is free software; see the source for copying conditions.  There 
> >=
> >is NO
> >=1B[0mwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR 
> >PU=
> >RPOSE.
> >=1B[0m
> >linux$ cat /etc/SuSE-release=20
> >SuSE Linux 9.3 (i586)
> >VERSION =3D 9.3
> >linux$ R --vanilla --debugger=3Dvalgrind < bar.R >| bar.Rout
> >=3D=3D22324=3D=3D Memcheck, a memory error detector for x86-linux.
> >=3D=3D22324=3D=3D Copyright (C) 2002-2004, and GNU GPL'd, by Julian Seward 
> >=
> >et al.
> >=3D=3D22324=3D=3D Using valgrind-2.2.0, a program supervision framework 
> >for=
> >x86-linux.
> >=3D=3D22324=3D=3D Copyright (C) 2000-2004, and GNU GPL'd, by Julian Seward 
> >=
> >et al.
> >=3D=3D22324=3D=3D For more details, rerun with: -v
> >=3D=3D22324=3D=3D=20
> >=3D=3D22324=3D=3D Invalid read of size 4
> >=3D=3D22324=3D=3D    at 0x81255AD: parse_expression (regex.c:5045)
> >=3D=3D22324=3D=3D    by 0x8125868: parse_branch (regex.c:4475)
> >=3D=3D22324=3D=3D    by 0x8125913: parse_reg_exp (regex.c:4420)
> >=3D=3D22324=3D=3D    by 0x81261B3: Rf_regcomp (regex.c:4384)
> >=3D=3D22324=3D=3D  Address 0x1C1E23A8 is 0 bytes after a block of size 32 
> >a=
> >lloc'd
> >=3D=3D22324=3D=3D    at 0x1B90650D: calloc (in 
> >/usr/lib/valgrind/vgpreload_=
> >memcheck.so)
> >=3D=3D22324=3D=3D    by 0x81247B5: parse_expression (regex.c:5406)
> >=3D=3D22324=3D=3D    by 0x8125868: parse_branch (regex.c:4475)
> >=3D=3D22324=3D=3D    by 0x8125913: parse_reg_exp (regex.c:4420)
> >=3D=3D22324=3D=3D=20
> >=3D=3D22324=3D=3D Invalid write of size 4
> >=3D=3D22324=3D=3D    at 0x81255B2: parse_expression (regex.c:5045)
> >=3D=3D22324=3D=3D    by 0x8125868: parse_branch (regex.c:4475)
> >=3D=3D22324=3D=3D    by 0x8125913: parse_reg_exp (regex.c:4420)
> >=3D=3D22324=3D=3D    by 0x81261B3: Rf_regcomp (regex.c:4384)
> >=3D=3D22324=3D=3D  Address 0x1C1E23A8 is 0 bytes after a block of size 32 
> >a=
> >lloc'd
> >=3D=3D22324=3D=3D    at 0x1B90650D: calloc (in 
> >/usr/lib/valgrind/vgpreload_=
> >memcheck.so)
> >=3D=3D22324=3D=3D    by 0x81247B5: parse_expression (regex.c:5406)
> >=3D=3D22324=3D=3D    by 0x8125868: parse_branch (regex.c:4475)
> >=3D=3D22324=3D=3D    by 0x8125913: parse_reg_exp (regex.c:4420)
> >=3D=3D22324=3D=3D=20
> >=3D=3D22324=3D=3D ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 39 
> >f=
> >rom 2)
> >=3D=3D22324=3D=3D malloc/free: in use at exit: 12691882 bytes in 6426 
> >block=
> >s.
> >=3D=3D22324=3D=3D malloc/free: 32534 allocs, 26108 frees, 33105500 bytes 
> >al=
> >located.
> >=3D=3D22324=3D=3D For a detailed leak analysis,  rerun with: --leak-check=
> >=3Dyes
> >=3D=3D22324=3D=3D For counts of detected errors, rerun with: -v
> >linux$ exit
> >
> >Script done on Mon 01 Aug 2005 02:10:42 PM PDT
> >---------- end of script ----------
> >--=20
> >Charles Geyer
> >Professor, School of Statistics
> >University of Minnesota
> >charlie at stat.umn.edu
> >
> >______________________________________________
> >R-devel at r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595

-- 
Charles Geyer
Professor, School of Statistics
University of Minnesota
charlie at stat.umn.edu



[Rd] valgrind complains about regex.c (PR#8043)
Charles Geyer