Re: [Rd] *** buffer overflow detected ***: /usr/lib64/R/bin/exec/R terminated on R 2.6.2 to 2.8.0: logging a bug?

From: Corrado <ct529_at_york.ac.uk>
Date: Fri, 31 Oct 2008 12:37:10 +0000

I apologise .... The dsn is not empty, the database the dsn connects to is empty!

You get the same error when connecting to a populated database.

Regards

On Friday 31 October 2008 12:26:39 Peter Dalgaard wrote:
> Corrado wrote:
> > Dear friends,
> >
> > there is a serious problem with RODBC on R from 2.6.2 to 2.8.0 on a
> > postgresql 8.3 database.
> >
> > Let's say we define an empty dsn called "test", with user "postgres" and
> > password "none". We test the connection with another application, and it
> > works properly.
> >
> > When you call the database using RODBC, you get the following:
> >> odbcConnect("test","postgres","none")
> >
> > *** buffer overflow detected ***: /usr/lib64/R/bin/exec/R terminated
> > ======= Backtrace: =========
> > /lib64/libc.so.6(__fortify_fail+0x37)[0x2ad38a3f4157]
> > /lib64/libc.so.6[0x2ad38a3f27e0]
> > /lib64/libc.so.6[0x2ad38a3f1db9]
> > /lib64/libc.so.6(_IO_default_xsputn+0x8e)[0x2ad38a379b5e]
> > /lib64/libc.so.6(_IO_vfprintf+0x3c22)[0x2ad38a351fa2]
> > /lib64/libc.so.6(__vsprintf_chk+0x9d)[0x2ad38a3f1e5d]
> > /lib64/libc.so.6(__sprintf_chk+0x80)[0x2ad38a3f1da0]
> > /usr/lib64/libodbcpsql.so.2(SQLGetInfo+0x973)[0x2ad38de11013]
> > /usr/lib64/libodbc.so.1(SQLGetInfo+0x624)[0x2ad38c5e91a4]
> > /usr/lib64/R/library/RODBC/libs/RODBC.so(RODBCGetInfo+0xbb)[0x2ad38c393a9
> >b]
>
> -....-
>
> > OS: Mandriva 2008.1 x86_64
> > Postgresql: 8.3.1 (PostGIS enabled)
> > R: from 2.6.2 from repository to 2.8.0 repackaged
> >
> > Is it my doing, or R's doing?
>
> (R-help snipped)
>
> It looks like that the problem is in the RODBC package, so the
> maintainer of RODBC should be informed. For reproducibility, you might
> need to be more explicit about how to create an "empty dsn" with postgres.

-- 
Corrado Topi

Global Climate Change & Biodiversity Indicators
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct529_at_york.ac.uk

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