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

dubravko.dolic at komdat.com dubravko.dolic at komdat.com
Mon Jun 6 11:57:44 CEST 2005

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
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.

Is anyone out there having similar problems in this environment. Any hints


Dubravko Dolic
Statistical Analyst
Tel:      +49 (0)89-55 27 44 - 4630
Fax:     +49 (0)89-55 27 44 - 2463
Email: dubravko.dolic at komdat.com
Komdat GmbH
Nymphenburger Straße 86
80636 München

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