[Rd] Segmentation fault using gentoo linux and mysql (PR#7919)

ripley at stats.ox.ac.uk ripley at stats.ox.ac.uk
Mon Jun 6 16:17:06 CEST 2005

This is most likely a problem with the package RMySQL and not with R.

On Mon, 6 Jun 2005 dubravko.dolic at komdat.com wrote:

> Full_Name: Dubravko Dolic
> Version: 2.1.0
> OS: Linux
> Submission from: (NULL) (
> I posted this mail to the HELP list earlier. Meanwhile we are quite shure that
> there must be a bug. Not nessecarily in R. But maybe we can get some hints how
> to track the problem using R. Currently we are trying something with the ATLAS
> lib according to Bug Report 7718 on this Repository.
> Now my problem again:
> We have a data server with some amounts of data which we try to analyze using R.
> Now having some MySQL databases with MySQL Ver 12.22 Distrib 4.0.24 and R 2.1.0
> compiled from sources on this machine:
> Fujitsu Siemens CELSIUS V810
> 4 GB RAM
> Dual AMD Opteron Processor 246
> Harddisk via SAN.
> (see user details:)
> sysname                         "Linux" <- gentoo linux
> release		"2.6.11-hardened-r13"                               version "#1 SMP Fri
> May 27 15:25:55 CEST 2005"                               machine 				"x86_64"
> Editor: Emacs with ESS 5.2.3
> While I can connect R to the database (RMySQL/DBI) and retrieve basic
> information (e.g. SHOW TABLE, DESCRIBE) it is not possible to send SQL Queries.
> The moment I try to do: res <- dbSendQuery(con, "select * from table") or any
> other SELECT statement R terminates and I receive a Segmentation Fault.

Please use gdb to trace where the fault is occurring: my guess is in 
RMySQL.so, in which case this is best discussed with the package 
maintainer (see the R FAQ, section on BUGS).

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

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