[R-sig-DB] RODBC with Oracle and 64-bit Linux (encore)

[Harlan Harris]

I wondered about the -1 too...

But nope, neither of these suggestions work...

> .Machine$sizeof.pointer
[1] 8
> hdl <- odbcConnect('ORACLE', rows_at_time=1)> sqlQuery(hdl, 'select name
from catalog.program where rownum < 2', rows_at_time=1, as.is=TRUE)
Error in odbcQuery(channel, query, rows_at_time) :
  Calloc could not allocate (-1 of 22816) memory

 -Harlan

On Thu, Nov 18, 2010 at 12:52 PM, Marc Schwartz <marc_schwartz using me.com>wrote:

> OK.  What is interesting, albeit, it may be a red herring, is the -1 in the
> error message. Is that an indication of an integer wrap around or something
> more subtle?
>
> Please be sure that you are running 64 bit R. Check the result of:
>
>   .Machine$sizeof.pointer
>
> It should return 8 if you are running 64 bit R. If it returns 4, you are
> running 32 bit R, which would conflict with the rest of the 64 bit tool
> chain.
>
> If by chance you are running 32 bit R, you will need to install 64 bit R
> and reinstall your CRAN packages, including RODBC, since any C/FORTRAN code
> would be compiled as 32 bit programs.
>
> Can you also perhaps try a query that should result in a small result set?
> Perhaps a single column from a single row?
>
>
> Marc
>
> On Nov 18, 2010, at 11:29 AM, Harlan Harris wrote:
>
> Quick response -- thanks! Nope, doesn't help.
>
> >  library(RODBC)
> > hdl <- odbcConnect('ORACLE', rows_at_time=1)
> > sqlQuery(hdl, 'select * from catalog.program where rownum < 10',
> rows_at_time=1)
> Error in odbcQuery(channel, query, rows_at_time) :
>   Calloc could not allocate (-1 of 22816) memory
>
>  -Harlan
>
> On Thu, Nov 18, 2010 at 12:26 PM, Marc Schwartz <marc_schwartz using me.com>wrote:
>
>> On Nov 18, 2010, at 11:15 AM, Harlan Harris wrote:
>>
>> > Hi all,
>> >
>> > I'm trying again to get the R<->Oracle toolchain to work on 64-bit Linux
>> > (CentOS 5/RHEL 5). As previously established, it's nearly impossible,
>> > although I'm awfully close now and just need one bit of help.
>> >
>> > Here's what works:
>> >
>> > I installed the 64-bit Oracle Instant Client Basic and ODBC rpms
>> (version
>> > 11.2.0.2.0).
>> > export ORACLE_HOME=/usr/lib/oracle/11.2/client64/
>> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ORACLE_HOME/lib
>> > export TNS_ADMIN=/etc/oracle
>> > set up /etc/oracle/tnsname.ora
>> >
>> > The version of unixODBC that's installed on Redhat 5 is 2.2.11. That
>> version
>> > is old and doesn't work with 64-bit Oracle Instant Client. Both Oracle
>> and
>> > Redhat are aware of this and stubbornly refuse to fix it. Therefore I
>> > installed easysoft's ODBC Oracle driver. Note that this costs something
>> like
>> > $2000 to license, but if you've got Oracle, you can probably pay for it.
>> >
>> > The easysoft driver installs to /usr/local/easysoft. It includes
>> unixODBC
>> > 2.2.12. (I uninstalled the factor 2.2.11 version)
>> >
>> > I confirmed that it was properly configured and working by running
>> > /usr/local/easysoft/unixODBC/bin/isql and querying my database. Username
>> and
>> > password are in /etc/odbc.ini.
>> >
>> > I symlinked /usr/local/easysoft/unixODBC/lib, /include, and /bin to
>> > /usr/local/lib, /include and /bin, respectively.
>> >
>> > Now I install RODBC from source. It seems to work, finding sql.h,
>> sqlext.h,
>> > and -lodbc.
>> >
>> >> library(RODBC)
>> >> hdl <- odbcConnect('ORACLE')
>> >> sqlQuery(hdl, 'select * from catalog.program where rownum < 10')
>> > Error in odbcQuery(channel, query, rows_at_time) :
>> >  Calloc could not allocate (-1 of 22816) memory
>> >
>> >
>> > So close! What am I missing?
>> >
>> > Thanks!
>> >
>> > -Harlan
>>
>>
>> Harlan, glad to see some progress, albeit at a notable cost.
>>
>> Try using 'rows_at_time = 1' in the calls to both odbcConnect() and
>> sqlQuery().
>>
>> I have found the need to use that setting, rather than the default 100, in
>> order to successfully retrieve data from our Oracle server on OSX.
>>
>> The smaller value may also help to workaround the memory allocation issue,
>> presuming that something more subtle is not going on.
>>
>> HTH,
>>
>> Marc Schwartz
>>
>>
>
>

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