R devel - Jun 2005 - Segmentation fault using gentoo linux and mysql (PR#7919)

Full_Name: Dubravko Dolic
Version: 2.1.0
OS: Linux
Submission from: (NULL) (212.18.9.161)


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.

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

Regards


Dubravko Dolic
Statistical Analyst
Tel:      +49 (0)89-55 27 44 - 4630
Fax:     +49 (0)89-55 27 44 - 2463
Email: dubravko.dolic@komdat.com
Komdat GmbH
Nymphenburger Stra?e 86
80636 M?nchen

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

On Mon, 6 Jun 2005 dubravko.dolic@komdat.com wrote:
> Full_Name: Dubravko Dolic
> Version: 2.1.0
> OS: Linux
> Submission from: (NULL) (212.18.9.161)
>
>
> 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@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

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

On Mon, 6 Jun 2005 dubravko.dolic@komdat.com wrote:
> Full_Name: Dubravko Dolic
> Version: 2.1.0
> OS: Linux
> Submission from: (NULL) (212.18.9.161)
>
>
> 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@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