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 13:50:51 +0100

Corrado wrote:
> 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.

Do I? I wouldn't know...

(You are _still_ not providing steps to reproduce the situation!)

The actual maintainer might know, though, so wait for him to chime in.

        -p

>
> 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.

>
>
>
-- 
   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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