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: Peter Dalgaard <P.Dalgaard_at_biostat.ku.dk>
Date: Fri, 31 Oct 2008 13:26:39 +0100

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)[0x2ad38c393a9b]

-....-
> 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.

-- 
   O__  ---- Peter Dalgaard             Ă˜ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk)              FAX: (+45) 35327907

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