[R] retrieving large columns using RODBC

[bogdan romocea]

This appears to be an SQL issue. Look for a way to speed up your
queries in Postgresql. I presume you haven't created an index on
'index', which means that every time you run your SELECT, Postgresql
is forced to do a full table scan (not good). If the index doesn't
solve the problem, look for some SQL help.


> -----Original Message-----
> From: Tamas K Papp [mailto:tpapp at princeton.edu] 
> Sent: Saturday, August 13, 2005 4:03 AM
> To: R-help mailing list
> Subject: [R] retrieving large columns using RODBC
> 
> 
> Hi,
> 
> I have a large table in Postgresql (result of an MCMC 
> simulation, with 1
> million rows) and I would like to retrive colums (correspond 
> to variables)
> using RODBC.  I have a column called "index" which is used to 
> order rows.
> 
> Unfortunately, sqlQuery can't return all the values from a 
> column at once
> (RODBC complains about lack of memory).  So I am using the 
> following code:
> 
> getcolumns <- function(channel, tablename, colnames, totalrows,
>                       ordered=TRUE,chunksize=1e5) {
>   r <- matrix(double(0),totalrows,length(colnames))
>   for (i in 1:ceiling(totalrows/chunksize)) {
>     cat(".")
>     r[((i-1)*chunksize+1):(i*chunksize)] <- as.matrix(
>       sqlQuery(channel, paste("SELECT", paste(colnames,collapse=", "),
>                               "FROM", tablename,
>                               "WHERE index <=", i*chunksize,
>                               "AND index >", (i-1)*chunksize,
>                               if (ordered) "ORDER BY index;" 
> else ";")))
>   }
>   cat("\n")
>   drop(r)                               # convert to vector if needed
> }
> 
> to retrieve it in chunks.  However, this is very slow -- 
> takes about 15
> minutes on my machine.  Is there a way to speed it up?
> 
> I am running Linux on a powerbook, RODBC version 1.1-4, R 2.1.1.  The
> machine has only 512 Mb of RAM.
> 
> Thanks,
> 
> Tamas
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>