[R-sig-DB] NULL data not mapped to NA with RODBC on 64-bit Mac OS X

[Marc Schwartz]

Hi Harlan,

I suspect that we will need to wait for Prof. Ripley to be able to look into this further. There may be subtle issues at play here and I would defer to his more intimate knowledge of the ODBC tool chain.

I do know that the Actual driver is both 32 and 64 bit in a single installation. However, I run R in 32 bit mode (don't need the extra address space, even though I now have 8Gb on my MacBook Pro), so have not encountered the 64 bit issues that you report here.

I have the same header file. Note that SQLLEN is a signed declaration below. It is defined as a 'long' generally and as a INT64 for 64 bit Windows. It would be 'unsigned long' or UINT64, respectively for an unsigned value.

One question for you however, which is do you know if you are booting the 32 bit or 64 bit OSX kernel on your Mac? Macs prior to mid-2010 (like mine) running Snow Leopard typically default to the 32 bit kernel, though can be 64 bit 'capable'. It depends upon various factors including the presence of a 64 bit EFI. Newer Macs now boot into the 64 bit kernel by default. I have seen some problems reported on older Macs where the default kernel was changed from 32 bit to 64 bit, resulting in subtle and not so subtle problems with some drivers. Booting to the 32 bit kernel still allows you to run 64 bit apps under Snow Leopard, just that the kernel and extensions are 32 bit.

Regards,

Marc


On Mar 23, 2011, at 2:29 PM, Harlan Harris wrote:

> Any thoughts? Is there someone else or somewhere else I might ask?
> 
> -Harlan
> 
> On Tue, Mar 22, 2011 at 1:31 PM, Harlan Harris <harlan using harris.name> wrote:
> 
>> Hello,
>> 
>> I seem to have hit a bug in RODBC on 64-bit versions of R on Mac OS X. I'm
>> running R 2.12.1, and using R to talk to Oracle and other databases using
>> RODBC 1.3-2. In 32-bit mode (R32), everything works. (The ODBC drivers are
>> the ones from Actual.) In 64-bit mode (R), it seems as if NULL data is not
>> being treated as missing. For example, a NULL value in an integer column is
>> being returned as a 0 instead, which is wrong/bad.
>> 
>> Diving into the code and Google a bit, it seems like an issue that's been
>> seen before in other contexts. Here's the relevant C code, from
>> RODBCFetchRows:
>> 
>>        for(row = thisHandle->rowsUsed;
>>        row < thisHandle->rowsFetched && j <= maximum;
>>        j++, row++)
>>        {
>>        thisHandle->rowsUsed++;
>>        if(j > blksize) {
>>            blksize *= 2;
>>            for (i = 0; i < nc; i++)
>>            SET_VECTOR_ELT(data, i,
>>                       lengthgets(VECTOR_ELT(data, i), blksize));
>>        }
>>        for (i = 0; i < nc; i++) {
>>            SQLLEN len = thisHandle->ColData[i].IndPtr[row];
>>            switch(thisHandle->ColData[i].DataType) {
>>            case SQL_DOUBLE:
>>            REAL(VECTOR_ELT(data, i))[j-1] =
>>                len == SQL_NULL_DATA ? NA_REAL :
>>                thisHandle->ColData[i].RData[row];
>>            break;
>> 
>> etc...
>> 
>> Googling for SQL_NULL_DATA and related terms finds this page, about the
>> same issue in a Python driver:
>> 
>> http://code.google.com/p/pyodbc/issues/detail?id=51
>> 
>> It appears as if SQLLEN might be unsigned in 64-bit builds, while
>> SQL_NULL_DATA is -1. Casting len to be an int rather than an unsigned int
>> seems to solve the problem for them.
>> 
>> On my machine, /usr/include/sqltypes.h starts like this:
>> 
>> /*
>> *  sqltypes.h
>> *
>> *  $Id: sqltypes.h,v 1.23 2007/10/07 13:27:13 source Exp $
>> *
>> *  ODBC typedefs
>> *
>> *  The iODBC driver manager.
>> 
>> and defines SQLLEN as follows:
>> 
>> #ifdef _WIN64
>> typedef INT64                   SQLLEN;
>> typedef UINT64                  SQLULEN;
>> typedef UINT64                  SQLSETPOSIROW;
>> #elif defined(STRICT_ODBC_TYPES)
>> typedef long                    SQLLEN;
>> typedef unsigned long           SQLULEN;
>> typedef unsigned short          SQLSETPOSIROW;
>> #else
>> #define SQLLEN                  long
>> #define SQLULEN                 unsigned long
>> #define SQLSETPOSIROW           unsigned short
>> #endif
>> 
>> Seems to me like SQLLEN should be signed, but apparently not?
>> 
>> Can anyone help? Thank you!
>> 
>> -Harlan