rmysql warning and its associated mysql error

Hi all,

Here are some details about my code:

- I use a mysql server where my whole database is stored,
- I'm doing a logistic regression with the package biglm
- my 'data function' just does a SQL request for the selected variables 
and then I read part of it with the function fetch:

MySQLdatafun<-function(reset=FALSE)
{
  if(reset)
  {
    beginRead <<- 0
    endRead <<- 0
    dbClearResult(resSQL)
    resSQL <<- dbSendQuery(con, SQLSelectExplVar)
    return(NULL)
  }

  if(endRead >= lengthData)
      return(NULL)

  beginRead<<-endRead+1
  endRead<<-endRead+min(chunksize, lengthData-endRead)

  mydata <<- data.frame(fetch(resSQL, n=endRead-beginRead+1), 
stringsAsFactors=TRUE)
 # BTW the last argument 'stringAsFactor' does not seem to work.

  for(i in 1:NCOL(mydata))
    if(class(mydata[1,i]) == "character")
      mydata[,i] <<- factor(mydata[,i])

  mydata
}

- what's really strange is the problem occurs when I add some code to 
the biglm package to compute the con/discordant percentage.

I can not yet upgrade to 2.8.0 since there is no version of the (d)com 
server for this version of R.

Thanks in advance

Christophe Dutang

2008/11/3 Jeffrey Horner <jeff.horner at vanderbilt.edu 
<mailto:jeff.horner at vanderbilt.edu>>

    christophe dutang wrote on 10/31/2008 03:28 PM:

        Hi,

        I'm currently experiencing problem with the combination of mysql
        / Rmysql /
        R when reading the result of a 'big' query. If I select only 4
        variables of
        my mysql table, the result dimension has 56972 rows, I read by
        pack of
        50000, namely the first of 50000 and the second of 6972. In this
        cas I do
        not get any DBI warning telling an error of mysql server. But If
        I read the
        21 variables of my table, the result dimension is then 56972 x
        21. In R, the
        first read of 50000 rows is fine but second stops after reading
        2182 rows...
        and a DBI warning is raised

        RS-DBI driver warning: (error while fetching rows)

        This problem was raised in 2003, cf.
        https://stat.ethz.ch/pipermail/r-help/2003-April/032708.html

        But I found here
        http://www.mysqlperformanceblog.com/2007/07/06/, that "If
        you do not check for error it can look as you've done with
        result set while
        you only processed a portion of it, which can cause rather hard
        to catch
        errors."

        Does anyone experience this problem? and know how to solve it?


    Try upgrading R to 2.8.0. <http://2.8.0.>

    Can you provide your code to the list... or pseudo code so that we
    can troubleshoot? Specifically are you calling fetch() or dbApply()?

    Jeff


        Thanks in advance

        Christophe Dutang


        PS : I use R 2.7.2 on windows XP pro with RMySQL_0.6-1 and a
        MySQL community
        server 5.0

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