Re: (Debian Bug 344248): R segfaults when pressing Delete (PR#8422)

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Re: (Debian Bug 344248): R segfaults when pressing Delete (PR#8422)

Prof Brian Ripley
On Wed, 21 Dec 2005 [hidden email] wrote:

>
> --CE+1k2dSO48ffgeK
> Content-Type: text/plain; charset=us-ascii
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>
> Resend after type in mailheader.  I have the bug on my system with
> yesterday's R 2.2.1. A library mismatch is still a likely cause.

This seems to be a readline 5.1 error.  I was unable to reproduce it with
4.3 or 5.0.

gdb) bt
#0  0xb7f4c942 in _rl_dispatch_callback () from
/usr/local/lib/libreadline.so.5
#1  0xb7f5fd82 in rl_callback_read_char () from
/usr/local/lib/libreadline.so.5
#2  0x0816b98b in Rstd_ReadConsole (prompt=0xb7f6fafc "", buf=0xbf8bb1ec "", len=1024,
     addtohistory=0) at /users/ripley/R/svn/R-devel/src/unix/sys-std.c:663

Switching the link from libreadline.so.5 back to libreadline.so.5.0 made
this behave again.

Can you confirm you are running rl5.1?  Given the segfault is readline not
in R itself, it is at the very least a change in behaviour in a supposedly
compatible version of a dynamic library so it seems to me the bug should
be assigned to readline not R.

Brian


>
> Dirk
>
> --
> Hell, there are no rules here - we're trying to accomplish something.
>                                                  -- Thomas A. Edison
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> Date: Wed, 21 Dec 2005 06:33:07 -0600
> To: r-bugs@[hidden email]
> CC: Ethan Glasser-Camp <[hidden email]>, [hidden email],
> Subject: Re: Bug#344248: R crashes when I press "Delete"
> In-Reply-To: <[hidden email]>
> References: <[hidden email]>
> X-Mailer: VM 7.19 under Emacs 21.4.1
> From: Dirk Eddelbuettel <[hidden email]>
> X-rewrote-sender: [hidden email]
>
>
> On 21 December 2005 at 01:50, Ethan Glasser-Camp wrote:
> | Package: r-base-core
> | Version: 2.2.1-1
> |
> | When I run R, I can cause a crash by simply pressing Delete. Backspace works
> | fine, and I can use ESS without problems.
>
> Uh-oh.
>
> | ethan@sundance:~$ R
> |
> | R : Copyright 2005, The R Foundation for Statistical Computing
> | Version 2.2.1  (2005-12-20 r36812)
> | ISBN 3-900051-07-0
> |
> | R is free software and comes with ABSOLUTELY NO WARRANTY.
> | You are welcome to redistribute it under certain conditions.
> | Type 'license()' or 'licence()' for distribution details.
> |
> | R is a collaborative project with many contributors.
> | Type 'contributors()' for more information and
> | 'citation()' on how to cite R or R packages in publications.
> |
> | Type 'demo()' for some demos, 'help()' for on-line help, or
> | 'help.start()' for an HTML browser interface to help.
> | Type 'q()' to quit R.
> |
> | [Previously saved workspace restored]
>
> Could you (temporarily) remove that file?
>
> | > Segmentation fault
> | ethan@sundance:~$
>
> That said, I just tried this where I seemed to have no ~/.RData file.
> Pressing <Deletet><Return> leads to a SegFault.
>
> I will pass this on R Core.
>
> Thanks for the bug report.
>
> Dirk
>
> |
> |
> | Here is a list of packages I thought might be relevant:
> |
> | $ dpkg -l r-* libreadline*
> | Desired=Unknown/Install/Remove/Purge/Hold
> | | Status=Not/Installed/Config-files/Unpacked/Failed-config/Half-installed
> | |/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad)
> | ||/ Name           Version        Description
> | +++-==============-==============-============================================
> | un  libreadline-co <none>         (no description available)
> | un  libreadline-de <none>         (no description available)
> | ii  libreadline-ru 1.8.3+1.8.4pre Readline interface for Ruby 1.8
> | ii  libreadline4   4.3-18         GNU readline and history libraries, run-time
> | un  libreadline4-d <none>         (no description available)
> | ii  libreadline5   5.1-1          GNU readline and history libraries, run-time
> | ii  libreadline5-d 5.1-1          GNU readline and history libraries, developm
> | ii  r-base         2.2.1-1        GNU R statistical computing language and env
> | ii  r-base-core    2.2.1-1        GNU R core of statistical computing language
> | un  r-base-dev     <none>         (no description available)
> | ii  r-base-html    2.2.1-1        GNU R html docs for statistical computing sy
> | ii  r-base-latex   2.2.1-1        GNU R LaTeX docs for statistical computing s
> | ii  r-cran-boot    1.2.24-1       GNU R package for bootstrapping functions fr
> | ii  r-cran-cluster 1.10.2-1       GNU R package for cluster analysis by Rousse
> | ii  r-cran-foreign 0.8.12-1       GNU R package to read/write data from other
> | ii  r-cran-gdata   2.1.2-1        GNU R package with data manipulation tools b
> | ii  r-cran-gplots  2.2.0-1        GNU R package with tools for plotting data b
> | un  r-cran-gregmis <none>         (no description available)
> | ii  r-cran-gtools  2.2.2-1        GNU R package with R programming tools by Gr
> | ii  r-cran-kernsmo 2.22.15-1      GNU R package for kernel smoothing and densi
> | ii  r-cran-lattice 0.12-11.1-1    GNU R package for 'Trellis' graphics
> | ii  r-cran-lattice 0.1.1-1        GNU R package of additional graphical displa
> | ii  r-cran-mgcv    1.3-12-1       GNU R package for multiple parameter smoothi
> | ii  r-cran-misc3d  0.3-1-1        GNU R collection of 3d plot functions and rg
> | ii  r-cran-nlme    3.1.62-1       GNU R package for (non-)linear mixed effects
> | ii  r-cran-quadpro 1.4.7-2        GNU R package for solving quadratic programm
> | ii  r-cran-rgl     0.65-1         GNU R package for three-dimensional visualis
> | ii  r-cran-rpart   3.1.27-1       GNU R package for recursive partitioning and
> | ii  r-cran-surviva 2.20-1         GNU R package for survival analysis
> | un  r-cran-tkrplot <none>         (no description available)
> | ii  r-cran-vr      7.2.23-1       GNU R package accompanying the Venables and
> | un  r-doc-html     <none>         (no description available)
> | ii  r-doc-info     2.2.1-1        GNU R info manuals statistical computing sys
> | un  r-doc-pdf      <none>         (no description available)
> | un  r-mathlib      <none>         (no description available)
> | ii  r-recommended  2.2.1-1        GNU R collection of recommended packages [me
> |
> |
> | Please let me know if there is anything else I can do to help.
> |
> | Ethan
>
> --
> Hell, there are no rules here - we're trying to accomplish something.
>                                                  -- Thomas A. Edison
>
> --CE+1k2dSO48ffgeK--
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

--
Brian D. Ripley,                  [hidden email]
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

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Re: (Debian Bug 344248): R segfaults when pressing Delete (PR#8422)

Dirk Eddelbuettel
<ripley <at> stats.ox.ac.uk> writes:
> Can you confirm you are running rl5.1?  Given the segfault is readline not

Yes: readline 5.1, just like the bug submitter (see at the very bottom).

> compatible version of a dynamic library so it seems to me the bug should
> be assigned to readline not R.

Looks like it, yes. And from looking at http://bugs.debian.org/libreadline5
it seems that the same behaviour was just found with gdb.

Thanks for the quick replies!

Dirk

> > | ii  libreadline-ru 1.8.3+1.8.4pre Readline interface for Ruby 1.8
> > | ii  libreadline4   4.3-18         GNU readline and history libraries,
run-time
> > | un  libreadline4-d <none>         (no description available)
> > | ii  libreadline5   5.1-1          GNU readline and history libraries,
run-time
> > | ii  libreadline5-d 5.1-1          GNU readline and history libraries,
developm
> > | ii  r-base         2.2.1-1        GNU R statistical computing language
and env
> > | ii  r-base-core    2.2.1-1        GNU R core of statistical computing
language

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Re: (Debian Bug 344248): R segfaults when pressing Delete (PR#8422)

Dirk Eddelbuettel
On Wed, Dec 21, 2005 at 02:48:25PM +0000, Dirk Eddelbuettel wrote:
> <ripley <at> stats.ox.ac.uk> writes:
> > Can you confirm you are running rl5.1?  Given the segfault is readline not
>
> Yes: readline 5.1, just like the bug submitter (see at the very bottom).

And a new Debian version libreadline5.1-3 (and now 5.1-4) fixes it. I assume
the patch makes it upstream too.

Dirk

> > compatible version of a dynamic library so it seems to me the bug should
> > be assigned to readline not R.
>
> Looks like it, yes. And from looking at http://bugs.debian.org/libreadline5
> it seems that the same behaviour was just found with gdb.
>
> Thanks for the quick replies!
>
> Dirk
>
> > > | ii  libreadline-ru 1.8.3+1.8.4pre Readline interface for Ruby 1.8
> > > | ii  libreadline4   4.3-18         GNU readline and history libraries,
> run-time
> > > | un  libreadline4-d <none>         (no description available)
> > > | ii  libreadline5   5.1-1          GNU readline and history libraries,
> run-time
> > > | ii  libreadline5-d 5.1-1          GNU readline and history libraries,
> developm
> > > | ii  r-base         2.2.1-1        GNU R statistical computing language
> and env
> > > | ii  r-base-core    2.2.1-1        GNU R core of statistical computing
> language
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

--
Hell, there are no rules here - we're trying to accomplish something.
                                                  -- Thomas A. Edison

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